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The Vibrant Philly Biotech Scene: Focus on Computer-Aided Drug Design and Gfree Bio, LLC

Posted in Bio Instrumentation in Experimental Life Sciences Research, BioSimilars, BioTechnology - Venture Creation, Computational Biology/Systems and Bioinformatics, Disease Biology, Drug Delivery Platform Technology, Global Partnering & Biotech Investment, Interviews with Scientific Leaders, Investment in Technological Breakthrough, Pharmaceutical Discovery, Pharmaceutical Industry Competitive Intelligence, Pharmaceutical R&D Investment, Small Molecules in Development of Therapeutic Drugs, Venture Capital, tagged #biotech, Aviva Lev-Ari, bioinvestment, Biomolecular structure, biotech incubator, biotech startup, Biotechnology, Biotechnology and Pharmaceuticals, collaboration, computational biology, Conditions and Diseases, health, molecular modeling, philadelphia, research, SBIR, science, startup, structural biology, Venture capital on February 10, 2015| Leave a Comment »

The Vibrant Philly Biotech Scene: Focus on Computer-Aided Drug Design and Gfree Bio, LLC

Curator: Stephen J. Williams, Ph.D.

Article ID #166: The Vibrant Philly Biotech Scene: Focus on Computer-Aided Drug Design and Gfree Bio, LLC. Published on 2/10/2015

WordCloud Image Produced by Adam Tubman

This post is the second in a series of posts highlighting interviews with Philadelphia area biotech startup CEO’s and show how a vibrant biotech startup scene is evolving in the city as well as the Delaware Valley area. Philadelphia has been home to some of the nation’s oldest biotechs including Cephalon, Centocor, hundreds of spinouts from a multitude of universities as well as home of the first cloned animal (a frog), the first transgenic mouse, and Nobel laureates in the field of molecular biology and genetics. Although some recent disheartening news about the fall in rankings of Philadelphia as a biotech hub and recent remarks by CEO’s of former area companies has dominated the news, biotech incubators like the University City Science Center and Bucks County Biotechnology Center as well as a reinvigorated investment community (like PCCI and MABA) are bringing Philadelphia back. And although much work is needed to bring the Philadelphia area back to its former glory days (including political will at the state level) there are many bright spots such as the innovative young companies as outlined in these posts.

In today’s post, I had the opportunity to talk with molecular modeler Charles H. Reynolds, Ph.D., founder and CEO of Gfree Bio LLC, a computational structure-based design and modeling company based in the Pennsylvania Biotech Center of Bucks County. Gfree is actually one of a few molecular modeling companies at the Bucks County Biotech Center (I highlighted another company RabD Biotech which structural computational methods to design antibody therapeutics).

Below is the interview with Dr. Reynolds of Gfree Bio LLC and Leaders in Pharmaceutical Business Intelligence (LPBI):

LPBI: Could you briefly explain, for non-molecular modelers, your business and the advantages you offer over other molecular modeling programs (either academic programs or other biotech companies)? As big pharma outsources more are you finding that your company is filling a needed niche market?

GfreeBio: Gfree develops and deploys innovative computational solutions to accelerate drug discovery. We can offer academic labs a proven partner for developing SBIR/STTR proposals that include a computational or structure-based design component. This can be very helpful in developing a successful proposal. We also provide the same modeling and structure-based design input for small biotechs that do not have these capabilities internally. Working with Gfree is much more cost-effective than trying to develop these capabilities internally. We have helped several small biotechs in the Philadelphia region assess their modeling needs and apply computational tools to advance their discovery programs. (see publication and collaboration list here).

LPBI: Could you offer more information on the nature of your 2014 STTR award?

GfreeBio: Gfree has been involved in three successful SBIR/STTR awards in 2014. I am the PI for an STTR with Professor Burgess of Texas A&M that is focused on new computational and synthetic approaches to designing inhibitors for protein-protein interactions. Gfree is also collaborating with the Wistar Institute and Phelix Therapeutics on two other Phase II proposals in the areas of oncology and infectious disease.

LPBI: Why did you choose the Bucks County Pennsylvania Biotechnology Center?

GfreeBio: I chose to locate my company at the Biotech Center because it is a regional hub for small biotech companies and it provides a range of shared resources that are very useful to the company. Many of my most valuable collaborations have resulted from contacts at the center.

LPBI: The Blumberg Institute and Natural Products Discovery Institute has acquired a massive phytochemical library. How does this resource benefit the present and future plans for GfreeBio?

GfreeBio: To date Gfree Bio has not been an active collaborator with the Natural Products Insititute, but I have a good relationship with the Director and that could change at any time.

LPBI: Was the state of Pennsylvania and local industry groups support GfreeBio’s move into the Doylestown incubator? Has the partnership with Ben Franklin Partners and the Center provided you with investment and partnership opportunities?

GfreeBio: Gfree Bio has not been actively seeking outside investors, at least to date. We have been focused on growing the company through collaborations and consulting relationships. However, we have benefitted from being part of the Keystone Innovation Zone, a state program that provides incentives for small technology-based businesses in Pennsylvania.

LPBI: You will be speaking at a conference in the UK on reinventing the drug discovery process through tighter collaborations between biotech, academia, and non-profit organizations. How do you feel the Philadelphia area can increase this type of collaboration to enhance not only the goals and missions of nonprofits, invigorate the Pennsylvania biotech industry, but add much needed funding to the local academic organizations?

GfreeBio: I think this type of collaboration across sectors appears to be one of the most important emerging models for drug discovery. The Philadelphia region has been in many ways hard hit by the shift of drug discovery from large vertically integrated pharmaceutical companies to smaller biotechs, since this area was at the very center of “Big Pharma.” But I think the region is bouncing back as it shifts more to being a center for biotech. The three ingredients for success in the new pharma model are great universities, a sizeable talent pool, and access to capital. The last item may be the biggest challenge locally. The KIZ program (Keystone Innovation Zone) is a good start, but the region and state could do more to help promote innovation and company creation. Some other states are being much more aggressive.

LPBI: In addition, the Pennsylvania Biotechnology Center in Bucks County appears to have this ecosystem: nonprofit organizations, biotechs, and academic researchers. Does this diversity of researchers/companies under one roof foster the type of collaboration needed, as will be discussed at the UK conference? Do you feel collaborations which are in close physical proximity are more effective and productive than a “virtual-style” (online) collaboration model? Could you comment on some of the collaborations GfreeBio is doing with other area biotechs and academics?

GfreeBio: I do think the “ecosystem” at the Pennsylvania Biotechnology Center is important in fostering new innovative companies. It promotes collaborations that might not happen otherwise, and I think close proximity is always a big plus. As I mentioned before, many of the current efforts of Gfree have come from contacts at the center. This includes SBIR/STTR collaborations and contract work for local small biotech companies.

LPBI: Thompson Reuters just reported that China’s IQ (Innovation Quotient) has risen dramatically with the greatest patents for pharmaceuticals and compounds from natural products. Have you or your colleagues noticed more competition or business from Chinese pharmaceutical companies?

GfreeBio: The rise of Asia, particularly China, has been one of the most significant recent trends in the pharmaceutical industry. Initially, this was almost exclusively in the CRO space, but now China is aggressively building a fully integrated domestic pharmaceutical industry.

LPBI: How can the Philadelphia ecosystem work closer together to support greater innovation?

GfreeBio: A lot has happened in recent years to promote innovation and company creation in the region. There could always be more opportunities for networking and collaboration within the Philadelphia community. Of course the biggest obstacle in this business is often financing. Philadelphia needs more public and private sources for investment in startups.

LPBI: Thank you Dr. Reynolds.

Please look for future posts in this series on the Philly Biotech Scene on this site

Also, if you would like your Philadelphia biotech startup to be highlighted in this series please contact me: sjwilliamspa@comcast.net or @StephenJWillia2.

Our site is read by ~ 570,000 readers, among them thousand international readers daily and followed by thousands of Twitter followers.

The Vibrant Philly Biotech Scene: Focus on Vaccines and Philimmune, LLC

Posted in Advanced Drug Manufacturing Technology, BioSimilars, Cancer and Current Therapeutics, Cancer Prevention: Research & Programs, Disease Biology, Small Molecules in Development of Therapeutic Drugs, Etiology, FDA, FDA Regulatory Affairs, Health Economics and Outcomes Research, Healthcare costs and reimbursement, Human Immune System in Health and in Disease, Immunodiagnostics, Infectious Disease & New Antibiotic Targets, Infectious Disease Immunodiagnostics, Innovation in Immunology Diagnostics, Innovations, Interviews with Scientific Leaders, Investment in Technological Breakthrough, Pharmaceutical Drug Discovery, Pharmaceutical R&D Investment, tagged @Biotech News, biotech startup, Biotechnology, breast cancer, Cancer - General, cervical cancer, Clinical trial, Conditions and Diseases, Drug development, Food and Drug Administration, health, immune activation, Infectious disease, medicine, Merck & Co Inc, philadelphia, Regulatory science, vaccines on December 10, 2014| Leave a Comment »

The Vibrant Philly Biotech Scene: Focus on Vaccines and Philimmune, LLC

Curator: Stephen J. Williams, Ph.D

Article ID #163: The Vibrant Philly Biotech Scene: Focus on Vaccines and Philimmune, LLC. Published on 12/10/2014

WordCloud Image Produced by Adam Tubman

I am intending to do a series of posts highlighting interviews with Philadelphia area biotech startup CEO’s and show how a vibrant biotech startup scene is evolving in the city as well as the Delaware Valley area. Philadelphia has been home to some of the nation’s oldest biotechs including Cephalon, Centocor, hundreds of spinouts from a multitude of universities as well as home of the first cloned animal (a frog), the first transgenic mouse, and Nobel laureates in the field of molecular biology and genetics. Although some recent disheartening news about the fall in rankings of Philadelphia as a biotech hub and recent remarks by CEO’s of former area companies has dominated the news, biotech incubators like the University City Science Center and Bucks County Biotechnology Center as well as a reinvigorated investment community (like PCCI and MABA) are bringing Philadelphia back. And although much work is needed to bring the Philadelphia area back to its former glory days (including political will at the state level) there are many bright spots such as the innovative young companies as outlined in these posts.

First up I got to talk with Florian Schodel, M.D., Ph.D., CEO of Philimmune, which provides expertise in medicine, clinical and regulatory development and analytical sciences to support successful development and registration of vaccines and biologics. Before founding Philimmune, Dr. Schodel was VP in Vaccines Clinical Research of Merck Research Laboratories and has led EU vaccine clinical trials and the clinical development of rotavirus, measles, mumps, hepatitis B, and rubella vaccines. In addition Dr. Schodel and Philimmune consult on several vaccine development efforts at numerous biotech companies including:

\His specialties and services include: vaccines and biologics development strategy, clinical development, clinical operations, strategic planning and alliances, international collaborations, analytical and assay development, project and portfolio integration and leadership.

Successful development of vaccines and biologics poses some unique challenges: including sterile manufacturing and substantial early capital investment before initiated clinical trials, assay development for clinical trial support, and unique trail design. Therefore vaccines and biologics development is a highly collaborative process between several disciplines.

The Philadelphia area has a rich history in vaccine development including the discovery and development of the rubella, cytomegaolovirus, a rabies, and the oral polio vaccine at the Wistar Institute. Dr. Schodel answered a few questions on the state of vaccine development and current efforts in the Philadelphia area, including recent efforts by companies such as GSK’s efforts and Inovio’s efforts developing an Ebola vaccine.

In his opinion, Dr. Schodel believes our biggest hurdle in vaccine development in a societal issue, not a preclinic development issue. Great advances have been made to speed the discovery process and enhance quality assurance of manufacture capabilities like

Making targets more immunogenic
Development strategies like “reverse vaccinology”

however there has not been a great history or support for developing vaccines for the plethora of infectious diseases seen in the developing world. As Dr. Schodel pointed out, there are relatively few players in the field, and tough to get those few players excited for investing in new targets.

However, some companies are rapidly expanding their vaccine portfolios including

GSK
Sanofi
Japanese companies are expanding their vaccine portfolios
Chinese companies are expanding their vaccine development efforts including for African-nation related diseases (see white paper on competition in China vaccine market)
Merck has supported hepatitis B vaccine distribution in China

Why haven’t 3^rd world countries developed their own vaccine programs?

Hard to find partners willing to invest and support development
Developing nations don’t have the money or infrastructure to support health programs
Doctors in these countries need to be educated on how to conduct trials, conduct vaccine programs like Gates Foundation does. For more information see Nature paper on obstacles to vaccine introduction in third world countries.

Lastly, Dr. Schodel touched on a growing area, cancer vaccine development. Recent advances in bladder cancer vaccine, cervical, and promising results in an early phase metastatic breast cancer vaccine trial and phase I oral cancer vaccine trial have reinvigorated this field of cancer vaccinology.

Historic Timeline of Vaccine Development

Graphic from http://en.pedaily.cn/Item.aspx?id=194125

Other posts on this site related to Biotech Startups in Philadelphia and some additional posts on infectious disease include:

RAbD Biotech Presents at 1st Pitch Life Sciences-Philadelphia

LytPhage Presents at 1st Pitch Life Sciences-Philadelphia

Hastke Inc. Presents at 1st Pitch Life Sciences-Philadelphia

1st Pitch Life Science- Philadelphia- What VCs Really Think of your Pitch

The History of Infectious Diseases and Epidemiology in the late 19th and 20th Century

Read Full Post »

Prefacing the e-Book Epilogue: Metabolic Genomics and Pharmaceutics

Posted in Academic Publishing, Atherogenic Processes & Pathology, Best evidence, Bio Instrumentation in Experimental Life Sciences Research, Biochemical pathways, Biological Networks, Gene Regulation and Evolution, tagged Alzheimers Disease, Apoptosis, ATP, Atrial fibrillation, Biochemistry and Molecular Biology, biomarkers, Biotechnology and Pharmaceuticals, Cancer research, Cardiovascular Disorders, Cell Biology, Conditions and Diseases on November 10, 2014| Leave a Comment »

Prefacing the e-Book Epilogue: Metabolic Genomics and Pharmaceutics

Author and Curator: Larry H. Bernstein, MD, FCAP

Adieu, adieu, adieu …

Sound of Music

Snoopy – Charlie happiness

This work has been a coming to terms with my scientific and medical end of career balancing in a difficult time after retiring, but it has been rewarding. In the clinical laboratories, radiology, anesthesiology, and in pharmacy, there has been some significant progress in support of surgical, gynecological, developmental, medical practices, and even neuroscience directed disciplines, as well as epidemiology over a period of half a century. Even then, cancer and neurological diseases have been most difficult because the scientific basic research has either not yet uncovered a framework, or because that framework has proved to be multidimensional. In the clinical laboratory sciences, there has been enormous progress in instrumental analysis, with the recent opening of molecular methods not yet prepared for routine clinical use, which will be a very great challenge to the profession, which has seen the development of large sample volume, multianalite, high-throughput, low-cost support emerging for decades. The capabilities now underway will also enrrich the the capabilities of the anatomic pathology suite and the capabilities of 3-dimensional radiological examination. In both pathology and radiology, we have seen the division of the fields into major subspecialties. The development of the electronic health record had to take lessons from the first developments in the separate developments of laboratory, radiology, and pharmacy health record systems, to which were added, full cardiology monitoring systems. These have been unintegrated. This made it difficult to bring forth a suitable patient health record because the information needed to support decision-making by practitioners was in separate “silos”. The mathematical methods that are being applied to the -OMICS sciences, can be brought to bear on the simplification and amplification of the clinicians’ ability to make decisions with near “errorless” discrimination, still allowing for an element of “art” in carrying out the history, physical examination, and knowledge unique to every patient.

We are at this time opening a very large, complex, study of biology in relationship to the human condition. This will require sufficient resources to be invested in the development of these for a better society, which I suspect, will go on beyond the life of my grandchildren. Hopefully, the long-term dangers of climate change will be controlled in that time. As a society, or as a group of interdependent societies, we have no long term interest in continuing self-destructive behaviors that have predominated in the history of mankind. I now top off these discussions with some further elucidation of what lies before us.

Metabolomics and systems pharmacology: why and how to model the human metabolic network for drug discovery

Douglas B. Kell and Royston Goodacre
School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
Drug Discovery Today Feb 2014;19(2) http://dx.doi.org/10.1016/j.drudis.2013.07.014

Metabolism represents the ‘sharp end’ of systems biology,

because changes in metabolite concentrations
are necessarily amplified relative to
changes in the transcriptome, proteome and enzyme activities,
which can be modulated by drugs.

To understand such behaviour, we therefore need
(and increasingly have)

reliable consensus (community) models of the human metabolic network
that include the important transporters.

Small molecule ‘drug’ transporters are in fact metabolite transporters,

because drugs bear structural similarities to metabolites known
from the network reconstructions and from measurements of the metabolome.

Recon2 represents the present state-of-the-art human metabolic
network reconstruction; it can predict inter alia:

the effects of inborn errors of metabolism;
which metabolites are exometabolites, and
how metabolism varies between tissues and cellular compartments.

Even these qualitative network models are not yet complete. As our
understanding improves so do we recognize more clearly the need for a systems (poly)pharmacology.

Modelling biochemical networks – why we do so
There are at least four types of reasons as to why one would wish to model a biochemical network:

Assessing whether the model is accurate, in the sense that it
reflects – or can be made to reflect – known experimental facts.
Establishing what changes in the model would improve the
consistency of its behaviour with experimental observations
and improved predictability, such as with respect to metabolite
concentrations or fluxes.
Analyzing the model, typically by some form of sensitivity
analysis, to understand which parts of the system contribute
most to some desired functional properties of interest.
Hypothesis generation and testing, enabling one to analyse
rapidly the effects of manipulating experimental conditions in
the model without having to perform complex and costly
experiments (or to restrict the number that are performed).

In particular, it is normally considerably cheaper to perform
studies of metabolic networks in silico before trying a smaller
number of possibilities experimentally; indeed for combinatorial
reasons it is often the only approach possible. Although
our focus here is on drug discovery, similar principles apply to the
modification of biochemical networks for purposes of ‘industrial’
or ‘white’ biotechnology.
Why we choose to model metabolic networks more than

transcriptomic or proteomic networks

comes from the recognition – made particularly clear

by workers in the field of metabolic control analysis

– that, although changes in the activities of individual enzymes tend to have

rather small effects on metabolic fluxes,
they can and do have very large effects on metabolite concentrations (i.e. the metabolome).

Modelling biochemical networks – how we do so

Although one could seek to understand the

time-dependent spatial distribution of signalling and metabolic substances within indivi
dual cellular compartments and
while spatially discriminating analytical methods such as Raman spectroscopy and
mass spectrometry do exist for the analysis of drugs in situ,

the commonest type of modelling, as in the spread of substances in
ecosystems,
assumes ‘fully mixed’ compartments and thus ‘pools’ of metabolites.

Although an approximation, this ‘bulk’ modelling will be necessary for complex ecosystems such as humans where, in addition to the need for tissue- and cell-specific models, microbial communities inhabit this superorganism and the
gut serves as a source for nutrients courtesy of these symbionts.

Topology and stoichiometry of metabolic networks as major constraints on fluxes
Given their topology, which admits a wide range of parameters for
delivering the same output effects and thereby reflects biological
robustness,

metabolic networks have two especially important constraints that assist their accurate modelling:

(i) the conservation of mass and charge, and
(ii) stoichiometric and thermodynamic constraints.

These are tighter constraints than apply to signalling networks.

New developments in modelling the human metabolic network
Since 2007, several groups have been developing improved but nonidentical models of the human metabolic network at a generalised level and in tissue-specific forms. Following a similar community-driven strategy in Saccharomyces cerevisiae, surprisingly similar to humans, and in Salmonella typhimurium,

we focus in particular on a recent consensus paper that provides a highly curated and semantically annotated model of the human metabolic network, termed

Recon2 (http://humanmetabolism.org/).

In this work, a substantial number of the major groups active in this area came together to provide a carefully and manually constructed/curated network, consisting of some 1789 enzyme-encoding genes, 7440 reactions and 2626 unique metabolites distributed over eight cellular compartments. A variety of dead-end metabolites and blocked reactions remain (essentially orphans and widows). But Recon2 was able to

account for some 235 inborn errors of metabolism,
a variety of metabolic ‘tasks’ (defined as a non-zero flux through a reaction or through a pathway leading to the production of a metabolite Q from a metabolite P).
filtering based on expression profiling allowed the construction of 65 cell-type-specific models.
Excreted or exometabolites are an interesting set of metabolites,
and Recon2 could predict successfully a substantial fraction of those

Role of transporters in metabolic fluxes

The uptake and excretion of metabolites between cells and their macrocompartments

requires specific transporters and in the order of one third of ‘metabolic’ enzymes,
and indeed of membrane proteins, are in fact transporters or equivalent.

What is of particular interest (to drug discovery), based on their structural similarities, is the increasing recognition (Fig. 3) that pharmaceutical drugs also

get into and out of cells by ‘hitchhiking’ on such transporters, and not –

to any significant extent –

by passing through phospholipid bilayer portions
of cellular membranes.

This makes drug discovery even more a problem of systems biology than of biophysics.

role of solute carriers and other transporters in cellular drug uptake

Two views of the role of solute carriers and other transporters in cellular drug uptake. (a) A more traditional view in which all so-called ‘passive’drug uptake occurs through any unperturbed bilayer portion of membrane that might be present.
(b) A view in which the overwhelming fraction of drug is taken up via solute transporters or other carriers that are normally used for the uptake of intermediary metabolites. Noting that the protein:lipid ratio of biomembranes is typically 3:1 to 1:1 and that proteins vary in mass and density (a typical density is 1.37 g/ml) as does their extension, for example, normal to the ca. 4.5 nm lipid bilayer region, the figure attempts to portray a section of a membrane with realistic or typical sizes and amounts of proteins and lipids. Typical protein areas when viewed normal to the membrane are 30%, membranes are rather more ‘mosaic’ than ‘fluid’ and there is some evidence that there might be no genuinely ‘free’ bulk lipids (typical phospholipid masses are 750 Da) in biomembranes that are uninfluenced by proteins. Also shown is a typical drug: atorvastatin (LipitorW) – with a molecular mass of 558.64 Da – for size comparison purposes. If proteins are modelled as
cylinders, a cylinder with a diameter of 3.6 nm and a length of 6 nm has a molecular mass of ca. 50 kDa. Note of course that in a ‘static’ picture we cannot show the dynamics of either phospholipid chains or lipid or protein diffusion.

‘Newly discovered’ metabolites and/or their roles

To illustrate the ‘unfinished’ nature even of Recon2, which concentrates on the metabolites created via enzymes encoded in the human genome, and leaving aside the more exotic metabolites of drugs and foodstuffs and the ‘secondary’ metabolites of microorganisms, there are several examples of interesting ‘new’ (i.e. more or less recently recognised) human metabolites or roles thereof that are worth highlighting, often from studies seeking biomarkers of various diseases – for caveats of biomarker discovery, which is not a topic that we are covering here, and the need for appropriate experimental design. In addition, classes of metabolites not well represented in Recon2 are oxidised molecules such as those caused by nonenzymatic reaction of metabolites with free radicals such as the hydroxyl radical generated by unliganded iron. There is also significant interest in using methods of determining small molecules such as those in the
metabolome (inter alia) for assessing the ‘exposome’, in other words all the potentially polluting agents to which an
individual has been exposed.

Recently discovered effects of metabolites on enzymes

Another combinatorial problem reflects the fact that in molecular enzymology it is not normally realistic to assess every possible metabolite to determine whether it is an effector (i.e.activator or inhibitor) of the enzyme under study. Typical proteins are highly promiscuous and there is increasing evidence for the comparative promiscuity of metabolites
and pharmaceutical drugs. Certainly the contribution of individual small effects of multiple parameter changes can have substantial effects on the potential flux through an overall pathway, which makes ‘bottom up’ modelling an inexact science. Even merely mimicking the vivo (in Escherichia coli) concentrations of K+, Na+, Mg2+, phosphate, glutamate, sulphate and Cl significantly modulated the activities of several enzymes tested relative to the ‘usual’ assay conditions. Consequently, we need to be alive to the possibility of many (potentially major) interactions of which we are as yet ignorant. One class of example relates to the effects of the very widespread post-translational modification on metabolic
enzyme activities.

A recent and important discovery (Fig. 4) is that a single transcriptome experiment, serving as a surrogate for fluxes through individual steps, provides a huge constraint on possible models, and predicts in a numerically tractable way and
with much improved accuracy the fluxes to exometabolites without the need for such a variable ‘biomass’ term. Other recent and related strategies that exploit modern advances in ‘omics and network biology to limit the search space in constraint-based metabolic modelling.

Fig 4. Workflow for expression-profile-constrained metabolic flux estimation

Genome-scale metabolic model with gene-protein-reaction relationships
Map absolute gene expression levels to reactions
Maximise correlation between absolute gene expression and metabolic flux
Predict fluxes to exometabolites
Compare predicted with experimental fluxes to exometabolites

Drug Discovery Today

The steps in a workflow that uses constraints based on (i) metabolic network stoichiometry and chemical reaction properties (both encoded in the model) plus, and (ii) absolute (RNA-Seq) transcript expression profiles to enable the
accurate modelling of pathway and exometabolite fluxes. .

Concluding remarks – the role of metabolomics in systems pharmacology

What is becoming increasingly clear, as we recognize that to understand living organisms in health and disease we must treat them as systems, is that we must bring together our knowledge of the topologies and kinetics of metabolic networks with our knowledge of the metabolite concentrations (i.e. metabolomes) and fluxes. Because of the huge constraints imposed on metabolism by reaction stoichiometries, mass conservation and thermodynamics, comparatively few well-chosen ‘omics measurements might be needed to do this reliably (Fig. 4). Indeed, a similar approach exploiting constraints has come to the fore in denovo protein folding and interaction studies.

What this leads us to in drug discovery is the need to develop and exploit a ‘systems pharmacology’ where multiple binding targets are chosen purposely and simultaneously. Along with other measures such as phenotypic screening, and the integrating of the full suite of e-science approaches, one can anticipate considerable improvements in the rate of discovery of safe and effective drugs.

Metabolomics: the apogee of the omics trilogy
Gary J.!Patti, Oscar Yanes and Gary Siuzdak

Metabolites, the chemical entities that are transformed during metabolism, provide a functional readout of cellular biochemistry. With emerging technologies in mass spectrometry, thousands of metabolites can now be
quantitatively measured from minimal amounts of biological material, which has thereby enabled systems-level analyses. By performing global metabolite profiling, also known as untargeted metabolomics, new discoveries linking cellular pathways to biological mechanism are being revealed and are shaping our understanding of cell biology, physiology and medicine.

Metabolites are small molecules that are chemically transformed during metabolism and, as such, they provide a functional readout of cellular state. Unlike genes and proteins, the functions of which are subject to epigenetic regulation and posttranslational modifications, respectively, metabolites serve as direct signatures of biochemical activity and are therefore easier to correlate with phenotype. In this context, metabolite profiling, or metabolomics, has become a powerful approach that has been widely adopted for clinical diagnostics.

The field of metabolomics has made remarkable progress within the past decade and has implemented new tools that have offered mechanistic insights by allowing for the correlation of biochemical changes with phenotype.

In this Innovation article, we first define and differentiate between the targeted and untargeted approaches to metabolomics. We then highlight the value of untargeted metabolomics in particular and outline a guide to performing such studies. Finally, we describe selected applications of un targeted metabolomics and discuss their potential in cell biology.

metabolites serve as direct signatures of biochemical activity

In some instances, it may be of interest to examine a defined set of metabolites by using a targeted approach.
In other cases, an untargeted or global approach may be taken in which as many metabolites as possible are measured and compared between samples without bias.
Ultimately, the number and chemical composition of metabolites to be studied is a defining attribute of any metabolomic experiment and shapes experimental design with respect to sample preparation and choice of instrumentation.

The targeted and untargeted workflow for LC/MS-based metabolomics.

a | In the triple quadrupole (QqQ)-based targeted metabolomic workflow, standard compounds for the metabolites of interest are first used to set up selected reaction monitoring methods. Here, optimal instrument voltages are determined and response curves are generated for absolute quantification. After the targeted methods have been established
on the basis of standard metabolites, metabolites are extracted from tissues, biofluids or cell cultures and analysed. The data output provides quantification only of those metabolites for which standard methods have been built.

b | In the untargeted metabolomic workflow, metabolites are first isolated from biological samples and subsequently analysed by liquid chromatography followed by mass spectrometry (LC/MS). After data acquisition, the results are processed by using bioinformatic software such as XCMS to perform nonlinear retention time alignment and identify peaks that are changing between the groups of samples measured. The m/z value s for the peaks of interest are searched in metabolite databases to obtain putative identifications. Putative identifications are then confirmed
by comparing tandem mass spectrometry (MS/MS) data and retention time data to that of standard compounds. The untargeted workflow is global in scope and outputs data related to comprehensive cellular metabolism.

Metabolic Biomarker and Kinase Drug Target Discovery in Cancer Using Stable Isotope-Based Dynamic Metabolic Profiling (SIDMAP)

László G. Boros1*, Daniel J. Brackett2 and George G. Harrigan3
1UCLA School of Medicine, Harbor-UCLA Research and Education Institute, Torrance, CA. 2Department of Surgery, University of Oklahoma Health Sciences Center & VA Medical Center, Oklahoma City, OK, 3Global High Throughput
Screening (HTS), Pharmacia Corporation, Chesterfield, MO.
Current Cancer Drug Targets, 2003, 3, 447-455.

Tumor cells respond to growth signals by the activation of protein kinases, altered gene expression and significant modifications in substrate flow and redistribution among biosynthetic pathways. This results in a proliferating phenotype
with altered cellular function. These transformed cells exhibit unique anabolic characteristics, which includes increased and preferential utilization of glucose through the non-oxidative steps of the pentose cycle for nucleic acid synthesis but limited denovo fatty acid synthesis and TCA cycle glucose oxidation. This primarily nonoxidative anabolic profile reflects an undifferentiated highly proliferative aneuploid cell phenotype and serves as a reliable metabolic biomarker to determine cell proliferation rate and the level of cell transformation/differentiation in response to drug treatment. Novel drugs effective in particular cancers exert their anti-proliferative effects by inducing significant reversions of a few specific non-oxidative anabolic pathways. Here we present evidence that cell transformation of various mechanisms is sustained by a unique
disproportional substrate distribution between the two branches of the pentose cycle for nucleic acid synthesis, glycolysis and the TCA cycle for fatty acid synthesis and glucose oxidation. This can be demonstrated by the broad labeling and unique specificity of [1,2-13C2]glucose to trace a large number of metabolites in the metabolome. Stable isotope-based dynamic metabolic profiles (SIDMAP) serve the drug discovery process by providing a powerful new tool that integrates the metabolome into a functional genomics approach to developing new drugs. It can be used in screening kinases and their metabolic targets, which can therefore be more efficiently characterized, speeding up and improving drug testing, approval and labeling processes by saving trial and error type study costs in drug testing.

Navigating the HumanMetabolome for Biomarker Identification and Design of Pharmaceutical Molecules

Irene Kouskoumvekaki and Gianni Panagiotou
Department of Systems Biology, Center for Biological Sequence Analysis, Building 208, Technical University of Denmark, Lyngby, Denmark
Hindawi Publishing Corporation Journal of Biomedicine and Biotechnology 2011, Article ID 525497, 19 pages
http://dx.doi.org:/10.1155/2011/525497

Metabolomics is a rapidly evolving discipline that involves the systematic study of endogenous small molecules that characterize the metabolic pathways of biological systems. The study of metabolism at a global level has the potential to contribute significantly to biomedical research, clinical medical practice, as well as drug discovery. In this paper, we present the most up-to-date metabolite and metabolic pathway resources, and we summarize the statistical, and machine-learning tools used for the analysis of data from clinical metabolomics.

Through specific applications on cancer, diabetes, neurological and other diseases, we demonstrate how these tools can facilitate diagnosis and identification of potential biomarkers for use within disease diagnosis. Additionally, we
discuss the increasing importance of the integration of metabolomics data in drug discovery. On a case-study based on the Human Metabolome Database (HMDB) and the Chinese Natural Product Database (CNPD), we demonstrate the close relatedness of the two data sets of compounds, and we further illustrate how structural similarity with human metabolites could assist in the design of novel pharmaceuticals and the elucidation of the molecular mechanisms of medicinal plants.

Metabolites are the byproducts of metabolism, which is itself the process of converting food energy to mechanical energy
or heat. Experts believe there are at least 3,000 metabolites that are essential for normal growth and development (primary metabolites) and thousands more unidentified (around 20,000, compared to an estimated 30,000 genes and 100,000 proteins) that are not essential for growth and development (secondary metabolites) but could represent prognostic, diagnostic, and surrogate markers for a disease state and a deeper understanding of mechanisms of disease.

Metabolomics, the study of metabolism at the global level, has the potential to contribute significantly to biomedical
research, and ultimately to clinical medical practice. It is a close counterpart to the genome, the transcriptome and the proteome. Metabolomics, genomics, proteomics, and other “-omics” grew out of the Human Genome Project, a massive research effort that began in the mid-1990s and culminated in 2003 with a complete mapping of all the genes in the human body. When discussing the clinical advantages of metabolomics, scientists point to the “real-world” assessment
of patient physiology that the metabolome provides since it can be regarded as the end-point of the “-omics” cascade. Other functional genomics technologies do not necessarily predict drug effects, toxicological response, or disease states at the phenotype but merely indicate the potential cause for phenotypical response. Metabolomics can bridge this information gap. The identification and measurement of metabolite profile dynamics of host changes provides the closest link to the various phenotypic responses. Thus it is clear that the global mapping of metabolic signatures pre- and postdrug treatment is a promising approach to identify possible functional relationships between medication and medical phenotype.

Human Metabolome Database (HMDB). Focusing on quantitative, analytic, or molecular scale information about
metabolites, the enzymes and transporters associated with them, as well as disease related properties the HMDB represents the most complete bioinformatics and chemoinformatics medical information database. It contains records for
thousands of endogenous metabolites identified by literature surveys (PubMed, OMIM, OMMBID, text books), data
mining (KEGG, Metlin, BioCyc) or experimental analyses performed on urine, blood, and cerebrospinal fluid samples.
The annotation effort is aided by chemical parameter calculators and protein annotation tools originally developed for
DrugBank.

A key feature that distinguishes the HMDB from other metabolic resources is its extensive support for higher level database searching and selecting functions. More than 175 hand-drawn-zoomable, fully hyperlinked human
metabolic pathway maps can be found in HMDB and all these maps are quite specific to human metabolism and
explicitly show the subcellular compartments where specific reactions are known to take place. As an equivalent to
BLAST the HMDB contains a structure similarity search tool for chemical structures and users may sketch or
paste a SMILES string of a query compound into the Chem-Query window. Submitting the query launches a
structure similarity search tool that looks for common substructures from the query compound that match the
HMDB’s metabolite database. The wealth of information and especially the extensive linkage to metabolic diseases
to normal and abnormal metabolite concentration ranges, to mutation/SNP data and to the genes, enzymes, reactions
and pathways associated with many diseases of interest makes the HMDB one the most valuable tool in the hands
of clinical chemists, nutritionists, physicians and medical geneticists.

Metabolomics in Drug Discovery and Polypharmacology Studies

Drug molecules generally act on specific targets at the cellular level, and upon binding to the receptors, they exert
a desirable alteration of the cellular activities, regarded as the pharmaceutical effect. Current drug discovery depends
largely on ransom screening, either high-throughput screening (HTS) in vitro, or virtual screening (VS) in silico. Because
the number of available compounds is huge, several druglikeness filters are proposed to reduce the number of compounds that need to be evaluated. The ability to effectively predict if a chemical compound is “drug-like” or “nondruglike” is, thus, a valuable tool in the design, optimization, and selection of drug candidates for development. Druglikeness is a general descriptor of the potential of a small molecule to become a drug. It is not a unified descriptor
but a global property of a compound processing many specific characteristics such as good solubility, membrane
permeability, half-life, and having a pharmacophore pattern to interact specifically with a target protein. These
characteristics can be reflected as molecular descriptors such as molecular weight, log P, the number of hydrogen bond
donors, the number of hydrogen-bond acceptors, the number of rotatable bonds, the number of rigid bonds, the
number of rings in a molecule, and so forth.

Metabolomics for the Study of Polypharmacology of Natural Compounds

Internationally, there is a growing and sustained interest from both pharmaceutical companies and public in medicine
from natural sources. For the public, natural medicine represent a holistic approach to disease treatment, with
potentially less side effects than conventional medicine. For the pharmaceutical companies, bioactive natural products
constitute attractive drug leads, as they have been optimized in a long-term natural selection process for optimal interaction with biomolecules. To promote the ecological survival of plants, structures of secondary products have evolved to interact with molecular targets affecting the cells, tissues and physiological functions in competing microorganisms,
plants, and animals. In this, respect, some plant secondary products may exert their action by resembling endogenous
metabolites, ligands, hormones, signal transduction molecules, or neurotransmitters and thus have beneficial
effects on humans.

Future Perspectives

Metabolomics, the study of metabolism at the global level, is moving to exciting directions.With the development ofmore
sensitive and advanced instrumentation and computational tools for data interpretation in the physiological context,
metabolomics have the potential to impact our understanding of molecular mechanisms of diseases. A state-of-theart
metabolomics study requires knowledge in many areas and especially at the interface of chemistry, biology, and
computer science. High-quality samples, improvements in automated metabolite identification, complete coverage of
the human metabolome, establishment of spectral databases of metabolites and associated biochemical identities, innovative experimental designs to best address a hypothesis, as well as novel computational tools to handle metabolomics data are critical hurdles that must be overcome to drive the inclusion of metabolomics in all steps of drug discovery and drug development. The examples presented above demonstrated that metabolite profiles reflect both environmental and genetic influences in patients and reveal new links between metabolites and diseases providing needed prognostic,diagnostic, and surrogate biomarkers. The integration of these signatures with other omic technologies is of utmost importance to characterize the entire spectrum of malignant phenotype.

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Twitter is Becoming a Powerful Tool in Science and Medicine

Posted in Academic Publishing, Clinical Diagnostics, Computational Biology/Systems and Bioinformatics, Conference Coverage with Social Media, Curation, Curation methodology, Digital HealthCare – biotech & internet joint ventures, Drug Toxicity, Evolutionary cognition, FDA, FDA Regulatory Affairs, Global Partnering & Biotech Investment, Health Economics and Outcomes Research, HealthCare IT, Interviews with Scientific Leaders, Investment in Technological Breakthrough, Personal Health Applications: Tech Innovations serves HealhCare, Pharmaceutical Analytics, Pharmaceutical Discovery, Pharmacologic toxicities, Regulated Clinical Trials: Design, Methods, Components and IRB related issues, Scientific & Biotech Conferences: Press Coverage, tagged #mobilehealth, #science2_0, @science 2_0, Adverse event, Aviva Lev-Ari, Cancer - General, cancer patient management, Clinical trial, Conditions and Diseases, Conference Coverage with Social Media, Content Curation, Curation methodology, Food and Drug Administration, health, https://twitter.com/#!/pharma_BI, medical devices and digital health, medicine, mobile applications, patient outcomes, patient-interaction, Pharmacovigilance, research, science, Social media, Social network, Twitter on November 6, 2014| Leave a Comment »

Twitter is Becoming a Powerful Tool in Science and Medicine

Curator: Stephen J. Williams, Ph.D.

Article ID #159: Twitter is Becoming a Powerful Tool in Science and Medicine. Published on 11/6/2014

WordCloud Image Produced by Adam Tubman

Updated 4/2016

Twitter.com

A recent Science article (Who are the science stars of Twitter?; Sept. 19, 2014) reported the top 50 scientists followed on Twitter. However, the article tended to focus on the use of Twitter as a means to develop popularity, a sort of “Science Kardashian” as they coined it. So the writers at Science developed a “Kardashian Index (K-Index) to determine scientists following and popularity on Twitter.

Now as much buzz Kim Kardashian or a Perez Hilton get on social media, their purpose is solely for entertainment and publicity purposes, the Science sort of fell flat in that it focused mainly on the use of Twitter as a metric for either promotional or public outreach purposes. A notable scientist was mentioned in the article, using Twitter feed to gauge the receptiveness of his presentation. In addition, relying on Twitter for effective public discourse of science is problematic as:

Twitter feeds are rapidly updated and older feeds quickly get buried within the “Twittersphere” = LIMITED EXPOSURE TIMEFRAME
Short feeds may not provide the access to appropriate and understandable scientific information (The Science Communication Trap) which is explained in The Art of Communicating Science: traps, tips and tasks for the modern-day scientist. “The challenge of clearly communicating the intended scientific message to the public is not insurmountable but requires an understanding of what works and what does not work.” – from Heidi Roop, G.-Martinez-Mendez and K. Mills

However, as highlighted below, Twitter, and other social media platforms are being used in creative ways to enhance the research, medical, and bio investment collaborative, beyond a simple news-feed. And the power of Twitter can be attributed to two simple features

Ability to organize – through use of the hashtag (#) and handle (@), Twitter assists in the very important task of organizing, indexing, and ANNOTATING content and conversations. A very great article on Why the Hashtag in Probably the Most Powerful Tool on Twitter by Vanessa Doctor explains how hashtags and # search may be as popular as standard web-based browser search. Thorough annotation is crucial for any curation process, which are usually in the form of database tags or keywords. The use of # and @ allows curators to quickly find, index and relate disparate databases to link annotated information together. The discipline of scientific curation requires annotation to assist in the digital preservation, organization, indexing, and access of data and scientific & medical literature. For a description of scientific curation methodologies please see the following links:

Please read the following articles on CURATION

The Methodology of Curation for Scientific Research Findings

Power of Analogy: Curation in Music, Music Critique as a Curation and Curation of Medical Research Findings – A Comparison

Science and Curation: The New Practice of Web 2.0

Information Analytics –

Multiple analytic software packages have been made available to analyze information surrounding Twitter feeds, including Twitter feeds from #chat channels one can set up to cover a meeting, product launch etc.. Some of these tools include:

Twitter Analytics – measures metrics surrounding Tweets including retweets, impressions, engagement, follow rate, …

Twitter Analytics – Hashtags.org – determine most impactful # for your Tweets For example, meeting coverage of bioinvestment conferences or startup presentations using #startup generates automatic retweeting by Startup tweetbot @StartupTweetSF.

Tweet Sentiment Analytics

Examples of Twitter Use

A. Scientific Meeting Coverage

The 2013 Society of Teachers of Family Medicine Annual Spring Conference. integrated social media with meeting proceedings to enhance conference engagement

In a paper entitled Twitter Use at a Family Medicine Conference: Analyzing #STFM13 authors Ranit Mishori, MD, Frendan Levy, MD, and Benjamin Donvan analyzed the public tweets from the 2013 Society of Teachers of Family Medicine (STFM) conference bearing the meeting-specific hashtag #STFM13. Thirteen percent of conference attendees (181 users) used the #STFM13 to share their thoughts on the meeting (1,818 total tweets) showing a desire for social media interaction at conferences but suggesting growth potential in this area. As we have also seen, the heaviest volume of conference-tweets originated from a small number of Twitter users however most tweets were related to session content.

However, as the authors note, although it is easy to measure common metrics such as number of tweets and retweets, determining quality of engagement from tweets would be important for gauging the value of Twitter-based social-media coverage of medical conferences.

Thea authors compared their results with similar analytics generated by the HealthCare Hashtag Project, a project and database of medically-related hashtag use, coordinated and maintained by the company Symplur. Symplur’s database includes medical and scientific conference Twitter coverage but also Twitter usuage related to patient care. In this case the database was used to compare meeting tweets and hashtag use with the 2012 STFM conference.

These are some of the published journal articles that have employed Symplur (www.symplur.com) data in their research of Twitter usage in medical conferences.

The impact of social media on a major international emergency medicine conference.
Neill, A., Cronin, J. J., Brannigan, D., O’Sullivan, R., & Cadogan, M. (2013). The impact of social media on a major international emergency medicine conference. Emergency Medicine Journal, emermed-2012. Chicago
Social media in radiology: early trends in Twitter microblogging at radiology’s largest international meeting.
Hawkins, C. M., Duszak, R., & Rawson, J. V. (2014). Social Media in Radiology: Early Trends in Twitter Microblogging at Radiology’s Largest International Meeting. Journal of the American College of Radiology, 11(4), 387-390.
International Urology Journal Club via Twitter: 12-Month Experience.
Thangasamy, I. A., Leveridge, M., Davies, B. J., Finelli, A., Stork, B., & Woo, H. H. (2014). International Urology Journal Club via Twitter: 12-Month Experience. European urology.
Use of social media in urology: data from the American Urological Association (AUA).
Loeb, S., Bayne, C. E., Frey, C., Davies, B. J., Averch, T. D., Woo, H. H., … & Eggener, S. E. (2014). Use of social media in urology: data from the American Urological Association (AUA). BJU international, 113(6), 993-998. Chicago.
Social media: A tool to spread information: A case study analysis of Twitter conversation at the Cardiac Society of Australia & New Zealand 61st Annual Scientific Meeting 2013.
Ferguson, C., Inglis, S. C., Newton, P. J., Cripps, P. J., Macdonald, P. S., & Davidson, P. M. (2014). Social media: A tool to spread information: A case study analysis of Twitter conversation at the Cardiac Society of Australia & New Zealand 61st Annual Scientific Meeting 2013. Collegian.

Here, at Leaders in Pharmaceutical Business Intelligence (LBPI) we have integrated our web site, Twitter handle (@pharma_BI), and meeting specific hashtags, with a unique methodology, to monitor and measure meeting participant engagement for various international meetings (please see our Press Coverage section of our site for more information). These meetings included the 2nd Annual Sachs Associates Cancer BioInvestment & Partnering Forum and the 14^th Annual Sachs Associates Global Forum.

B. Twitter Usage for Patient Care and Engagement

Although the desire of patients to use and interact with their physicians over social media is increasing, along with increasing health-related social media platforms and applications, there are certain obstacles to patient-health provider social media interaction, including lack of regulatory framework as well as database and security issues. Some of the successes and issues of social media and healthcare are discussed in the post Can Mobile Health Apps Improve Oral-Chemotherapy Adherence? The Benefit of Gamification.

However there is also a concern if social media truly engages the patient and improves patient education. In a study of Twitter communications by breast cancer patients Tweeting about breast cancer, authors noticed Tweeting was a singular event. The majority of tweets did not promote any specific preventive behavior. The authors concluded “Twitter is being used mostly as a one-way communication tool.” (Using Twitter for breast cancer prevention: an analysis of breast cancer awareness month. Thackeray R¹, Burton SH, Giraud-Carrier C, Rollins S, Draper CR. BMC Cancer. 2013;13:508).

In addition a new poll by Harris Interactive and HealthDay shows one third of patients want some mobile interaction with their physicians.

Some papers cited in Symplur’s HealthCare Hashtag Project database on patient use of Twitter include:

e-Patients in Twitter Hashtag Communities.
Harmel M, Young K. e-Patients in twitter hashtag communities . J Participat Med. 2013 Jan 16; 5:e22
Nurses and Twitter: The good, the bad, and the reluctant.
Wilson, R., Ranse, J., Cashin, A., & McNamara, P. (2013). Nurses and Twitter: The good, the bad, and the reluctant. Collegian. Chicago.
Using social media for continuous professional development.
Moorley, C., & Chinn, T. (2014). Using social media for continuous professional development. Journal of advanced nursing.
Networking opportunities for learning disability nurses.
Abdulla, S., Marsden, D., Wilson, S., & Parker, M. (2013). Networking opportunities for learning disability nurses: Samuel Abdulla and colleagues explain why social media offer professionals new opportunities for information sharing, discussion and peer support. Learning Disability Practice, 16(5), 30-32.
Using Twitter for professional knowledge.
Kraft, M. A. (2013). Using Twitter for professional knowledge. Journal of the European Association for Health Information and Libraries, 9(4), 10.
A Study on the Influence of Semantics on the Analysis of Micro-blog Tags in the Medical Domain.
Vicient, C., & Moreno, A. (2013). A Study on the Influence of Semantics on the Analysis of Micro-blog Tags in the Medical Domain. In Availability, Reliability, and Security in Information Systems and HCI (pp. 446-459). Springer Berlin Heidelberg.
Twitter for Public Health: An Open-source Data Solution.
Nghiema, S., Mehtab, P., & Taoc, L. Twitter for Public Health: An Open-source Data Solution. Chicago.

C. Twitter Use in Pharmacovigilance to Monitor Adverse Events

Pharmacovigilance is the systematic detection, reporting, collecting, and monitoring of adverse events pre- and post-market of a therapeutic intervention (drug, device, modality e.g.). In a Cutting Edge Information Study, 56% of pharma companies databases are an adverse event channel and more companies are turning to social media to track adverse events (in Pharmacovigilance Teams Turn to Technology for Adverse Event Reporting Needs). In addition there have been many reports (see Digital Drug Safety Surveillance: Monitoring Pharmaceutical Products in Twitter) that show patients are frequently tweeting about their adverse events.

There have been concerns with using Twitter and social media to monitor for adverse events. For example FDA funded a study where a team of researchers from Harvard Medical School and other academic centers examined more than 60,000 tweets, of which 4,401 were manually categorized as resembling adverse events and compared with the FDA pharmacovigilance databases. Problems associated with such social media strategy were inability to obtain extra, needed information from patients and difficulty in separating the relevant Tweets from irrelevant chatter. The UK has launched a similar program called WEB-RADR to determine if monitoring #drug_reaction could be useful for monitoring adverse events. Many researchers have found the adverse-event related tweets “noisy” due to varied language but had noticed many people do understand some principles of causation including when adverse event subsides after discontinuing the drug.

However Dr. Clark Freifeld, Ph.D., from Boston University and founder of the startup Epidemico, feels his company has the algorithms that can separate out the true adverse events from the junk. According to their web site, their algorithm has high accuracy when compared to the FDA database. Dr. Freifeld admits that Twitter use for pharmacovigilance purposes is probably a starting point for further follow-up, as each patient needs to fill out the four-page forms required for data entry into the FDA database.

D. Use of Twitter in Big Data Analytics

Published on Aug 28, 2012

http://blogs.ischool.berkeley.edu/i29…

Course: Information 290. Analyzing Big Data with Twitter
School of Information
UC Berkeley

Lecture 1: August 23, 2012

Course description:
How to store, process, analyze and make sense of Big Data is of increasing interest and importance to technology companies, a wide range of industries, and academic institutions. In this course, UC Berkeley professors and Twitter engineers will lecture on the most cutting-edge algorithms and software tools for data analytics as applied to Twitter microblog data. Topics will include applied natural language processing algorithms such as sentiment analysis, large scale anomaly detection, real-time search, information diffusion and outbreak detection, trend detection in social streams, recommendation algorithms, and advanced frameworks for distributed computing. Social science perspectives on analyzing social media will also be covered.

This is a hands-on project course in which students are expected to form teams to complete intensive programming and analytics projects using the real-world example of Twitter data and code bases. Engineers from Twitter will help advise student projects, and students will have the option of presenting their final project presentations to an audience of engineers at the headquarters of Twitter in San Francisco (in addition to on campus). Project topics include building on existing infrastructure tools, building Twitter apps, and analyzing Twitter data. Access to data will be provided.

Other posts on this site on USE OF SOCIAL MEDIA AND TWITTER IN HEALTHCARE and Conference Coverage include:

Methodology for Conference Coverage using Social Media: 2014 MassBio Annual Meeting 4/3 – 4/4 2014, Royal Sonesta Hotel, Cambridge, MA

Strategy for Event Joint Promotion: 14th ANNUAL BIOTECH IN EUROPE FORUM For Global Partnering & Investment 9/30 – 10/1/2014 • Congress Center Basel – SACHS Associates, London

REAL TIME Cancer Conference Coverage: A Novel Methodology for Authentic Reporting on Presentations and Discussions launched via Twitter.com @ The 2nd ANNUAL Sachs Cancer Bio Partnering & Investment Forum in Drug Development, 19th March 2014 • New York Academy of Sciences • USA

PCCI’s 7th Annual Roundtable “Crowdfunding for Life Sciences: A Bridge Over Troubled Waters?” May 12 2014 Embassy Suites Hotel, Chesterbrook PA 6:00-9:30 PM

CRISPR-Cas9 Discovery and Development of Programmable Genome Engineering – Gabbay Award Lectures in Biotechnology and Medicine – Hosted by Rosenstiel Basic Medical Sciences Research Center, 10/27/14 3:30PM Brandeis University, Gerstenzang 121

Tweeting on 14th ANNUAL BIOTECH IN EUROPE FORUM For Global Partnering & Investment 9/30 – 10/1/2014 • Congress Center Basel – SACHS Associates, London

http://pharmaceuticalintelligence.com/press-coverage/

Statistical Analysis of Tweet Feeds from the 14th ANNUAL BIOTECH IN EUROPE FORUM For Global Partnering & Investment 9/30 – 10/1/2014 • Congress Center Basel – SACHS Associates, London

1st Pitch Life Science- Philadelphia- What VCs Really Think of your Pitch

What VCs Think about Your Pitch? Panel Summary of 1st Pitch Life Science Philly

How Social Media, Mobile Are Playing a Bigger Part in Healthcare

Can Mobile Health Apps Improve Oral-Chemotherapy Adherence? The Benefit of Gamification.

Medical Applications and FDA regulation of Sensor-enabled Mobile Devices: Apple and the Digital Health Devices Market

E-Medical Records Get A Mobile, Open-Sourced Overhaul By White House Health Design Challenge Winners

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Imaging-guided cancer treatment

Posted in Bio Instrumentation in Experimental Life Sciences Research, Biological Networks, Biomarkers & Medical Diagnostics, Biomedical Measurement Science, CANCER BIOLOGY & Innovations in Cancer Therapy, CE Mark & Global Regulatory Affairs: process management and strategic planning - GCP, Chemical Biology and its relations to Metabolic Disease, Chemical Genetics, Coagulation Therapy and Internal Bleeding, Components and IRB related issues, Computational Biology/Systems and Bioinformatics, CT, Disease Biology, Drug Delivery Platform Technology, Ecosystems & Industrial Concentration in the Medical Device Sector, FDA, FDA Regulatory Affairs, Gene Regulation and Evolution, Genetics & Pharmaceutical, GLP, Health Economics and Outcomes Research, Healthcare costs and reimbursement, Human Immune System in Health and in Disease, Image Processing/Computing, Imaging-based Cancer Patient Management, Innovation in Immunology Diagnostics, ISO 14155, Medical and Population Genetics, Medical Devices R&D and Inventions, Medical Devices R&D Investment, Medical Imaging Technology, Methods, Molecular Genetics & Pharmaceutical, MRI, Nanotechnology for Drug Delivery, Nuclear Medicine, Personalized and Precision Medicine & Genomic Research, Population Health Management, Regulated Clinical Trials: Design, Methods, Components and IRB related issues, Reproductive Biology & Bio Instrumentation, Resident-cell-based, Small Molecules in Development of Therapeutic Drugs, Technology Advance Assessment of, Technology Transfer: Biotech and Pharmaceutical, Translational Research, Translational Science, Ultra Sound, tagged Biochemistry and Molecular Biology, biomarkers, breast cancer, Cancer - General, Cancer research, Cell Biology, Chemotherapy, clinical imaging, Clinical trial, Clinical Trials, Conditions and Diseases, DNA, DNA Sequencing, gene, gene expression, genetics, health, imaging guided therapy, Lung cancer, Magnetic resonance imaging, mammography, medicine, Melanoma, Metabolism, Metabolomics, MRI, nanotechnology, ovarian cancer, Personalized medicine, Prostate cancer, Prostate-specific antigen, research, science, surgery, Therapy on September 30, 2014| Leave a Comment »

Imaging-guided cancer treatment

Writer & reporter: Dror Nir, PhD

It is estimated that the medical imaging market will exceed $30 billion in 2014 (FierceMedicalImaging). To put this amount in perspective; the global pharmaceutical market size for the same year is expected to be ~$1 trillion (IMS) while the global health care spending as a percentage of Gross Domestic Product (GDP) will average 10.5% globally in 2014 (Deloitte); it will reach ~$3 trillion in the USA.

Recent technology-advances, mainly miniaturization and improvement in electronic-processing components is driving increased introduction of innovative medical-imaging devices into critical nodes of major-diseases’ management pathways. Consequently, in contrast to it’s very small contribution to global health costs, medical imaging bears outstanding potential to reduce the future growth in spending on major segments in this market mainly: Drugs development and regulation (e.g. companion diagnostics and imaging surrogate markers); Disease management (e.g. non-invasive diagnosis, guided treatment and non-invasive follow-ups); and Monitoring aging-population (e.g. Imaging-based domestic sensors).

In; The Role of Medical Imaging in Personalized Medicine I discussed in length the role medical imaging assumes in drugs development. Integrating imaging into drug development processes, specifically at the early stages of drug discovery, as well as for monitoring drug delivery and the response of targeted processes to the therapy is a growing trend. A nice (and short) review highlighting the processes, opportunities, and challenges of medical imaging in new drug development is: Medical imaging in new drug clinical development.

The following is dedicated to the role of imaging in guiding treatment.

Precise treatment is a major pillar of modern medicine. An important aspect to enable accurate administration of treatment is complementing the accurate identification of the organ location that needs to be treated with a system and methods that ensure application of treatment only, or mainly to, that location. Imaging is off-course, a major component in such composite systems. Amongst the available solution, functional-imaging modalities are gaining traction. Specifically, molecular imaging (e.g. PET, MRS) allows the visual representation, characterization, and quantification of biological processes at the cellular and subcellular levels within intact living organisms. In oncology, it can be used to depict the abnormal molecules as well as the aberrant interactions of altered molecules on which cancers depend. Being able to detect such fundamental finger-prints of cancer is key to improved matching between drugs-based treatment and disease. Moreover, imaging-based quantified monitoring of changes in tumor metabolism and its microenvironment could provide real-time non-invasive tool to predict the evolution and progression of primary tumors, as well as the development of tumor metastases.

A recent review-paper: Image-guided interventional therapy for cancer with radiotherapeutic nanoparticles nicely illustrates the role of imaging in treatment guidance through a comprehensive discussion of; Image-guided radiotherapeutic using intravenous nanoparticles for the delivery of localized radiation to solid cancer tumors.

Abstract

One of the major limitations of current cancer therapy is the inability to deliver tumoricidal agents throughout the entire tumor mass using traditional intravenous administration. Nanoparticles carrying beta-emitting therapeutic radionuclides [DN: radioactive isotops that emits electrons as part of the decay process a list of β-emitting radionuclides used in radiotherapeutic nanoparticle preparation is given in table1 of this paper.) that are delivered using advanced image-guidance have signiﬁcant potential to improve solid tumor therapy. The use of image-guidance in combination with nanoparticle carriers can improve the delivery of localized radiation to tumors. Nanoparticles labeled with certain beta-emitting radionuclides are intrinsically theranostic agents that can provide information regarding distribution and regional dosimetry within the tumor and the body. Image-guided thermal therapy results in increased uptake of intravenous nanoparticles within tumors, improving therapy. In addition, nanoparticles are ideal carriers for direct intratumoral infusion of beta-emitting radionuclides by convection enhanced delivery, permitting the delivery of localized therapeutic radiation without the requirement of the radionuclide exiting from the nanoparticle. With this approach, very high doses of radiation can be delivered to solid tumors while sparing normal organs. Recent technological developments in image-guidance, convection enhanced delivery and newly developed nanoparticles carrying beta-emitting radionuclides will be reviewed. Examples will be shown describing how this new approach has promise for the treatment of brain, head and neck, and other types of solid tumors.

The challenges this review discusses

intravenously administered drugs are inhibited in their intratumoral penetration by high interstitial pressures which prevent diffusion of drugs from the blood circulation into the tumor tissue [1–5].
relatively rapid clearance of intravenously administered drugs from the blood circulation by kidneys and liver.
drugs that do reach the solid tumor by diffusion are inhomogeneously distributed at the micro-scale – This cannot be overcome by simply administering larger systemic doses as toxicity to normal organs is generally the dose limiting factor.
even nanoparticulate drugs have poor penetration from the vascular compartment into the tumor and the nanoparticles that do penetrate are most often heterogeneously distributed

How imaging could mitigate the above mentioned challenges

The inclusion of an imaging probe during drug development can aid in determining the clearance kinetics and tissue distribution of the drug non-invasively. Such probe can also be used to determine the likelihood of the drug reaching the tumor and to what extent.

Note: Drugs that have increased accumulation within the targeted site are likely to be more effective as compared with others. In that respect, Nanoparticle-based drugs have an additional advantage over free drugs with their potential to be multifunctional carriers capable of carrying both therapeutic and diagnostic imaging probes (theranostic) in the same nanocarrier. These multifunctional nanoparticles can serve as theranostic agents and facilitate personalized treatment planning.

Imaging can also be used for localization of the tumor to improve the placement of a catheter or external device within tumors to cause cell death through thermal ablation or oxidative stress secondary to reactive oxygen species.

See the example of Vintfolide in The Role of Medical Imaging in Personalized Medicine

Note: Image guided thermal ablation methods include radiofrequency (RF) ablation, microwave ablation or high intensity focused ultrasound (HIFU). Photodynamic therapy methods using external light devices to activate photosensitizing agents can also be used to treat superﬁcial tumors or deeper tumors when used with endoscopic catheters.

Quality control during and post treatment

For example: The use of high intensity focused ultrasound (HIFU) combined with nanoparticle therapeutics: HIFU is applied to improve drug delivery and to trigger drug release from nanoparticles. Gas-bubbles are playing the role of the drug’s nano-carrier. These are used both to increase the drug transport into the cell and as ultrasound-imaging contrast material. The ultrasound is also used for processes of drug-release and ablation.

Additional example; Multifunctional nanoparticles for tracking CED (convection enhanced delivery) distribution within tumors: Nanoparticle that could serve as a carrier not only for the therapeutic radionuclides but simultaneously also for a therapeutic drug and 4 different types of imaging contrast agents including an MRI contrast agent, PET and SPECT nuclear diagnostic imaging agents and optical contrast agents as shown below. The ability to perform multiple types of imaging on the same nanoparticles will allow studies investigating the distribution and retention of nanoparticles initially in vivo using non-invasive imaging and later at the histological level using optical imaging.

Conclusions

Image-guided radiotherapeutic nanoparticles have signiﬁcant potential for solid tumor cancer therapy. The current success of this therapy in animals is most likely due to the improved accumulation, retention and dispersion of nanoparticles within solid tumor following image-guided therapies as well as the micro-ﬁeld of the β-particle which reduces the requirement of perfectly homogeneous tumor coverage. It is also possible that the intratumoral distribution of nanoparticles may beneﬁt from their uptake by intratumoral macrophages although more research is required to determine the importance of this aspect of intratumoral radionuclide nanoparticle therapy. This new approach to cancer therapy is a fertile ground for many new technological developments as well as for new understandings in the basic biology of cancer therapy. The clinical success of this approach will depend on progress in many areas of interdisciplinary research including imaging technology, nanoparticle technology, computer and robot assisted image-guided application of therapies, radiation physics and oncology. Close collaboration of a wide variety of scientists and physicians including chemists, nanotechnologists, drug delivery experts, radiation physicists, robotics and software experts, toxicologists, surgeons, imaging physicians, and oncologists will best facilitate the implementation of this novel approach to the treatment of cancer in the clinical environment. Image-guided nanoparticle therapies including those with β-emission radionuclide nanoparticles have excellent promise to significantly impact clinical cancer therapy and advance the ﬁeld of drug delivery.

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Pfizer Cambridge Collaborative Innovation Events: ‘The Role of Innovation Districts in Metropolitan Areas to Drive the Global an | Basecamp Business

Posted in Advanced Drug Manufacturing Technology, Bio Instrumentation in Experimental Life Sciences Research, Biomedical Measurement Science, Health Economics and Outcomes Research, Innovation in Immunology Diagnostics, International Global Work in Pharmaceutical, Medical Devices R&D Investment, Pharmaceutical Industry Competitive Intelligence, tagged Biomedical Engineering, Biotechnology and Pharmaceuticals, Conditions and Diseases, innovation in health, innovation in healthcare, open innovation, Pfizer on September 7, 2014| Leave a Comment »

Pfizer Cambridge Collaborative Innovation Events: ‘The Role of Innovation Districts in Metropolitan Areas to Drive the Global an | Basecamp Business.

Reporter: Stephen J. Williams, Ph.D.

Monday, September 8 2014 5:30pm – 7:00pm Other Time Presented by:

Pfizer Cambridge/Boston Site Head

Event Details:
Date/Time: Monday, September 8, 2014, 5:30-7PM EDT
Venue: Pfizer Cambridge Seminar Room (ground floor)
Location: Pfizer Inc., 610 Main Street, Cambridge, MA 02139 . Click here for a map to the location.
(Corner of Portland and Albany street, Cambridge, MA 02139)
RSVP: To confirm your attendance please RSVP online through this website. This is an ONLINE REGISTRATION-ONLY event (there will not be registration at the door).

The Role of Innovation Districts in Metropolitan Areas to Drive the Global and Local Economy: Cambridge/Boston Case Study

Join Pfizer Cambridge at our new residence for a fascinating evening led by Vise-President and Founding Director, Bruce Katz of Brookings Institution, followed by a networking reception with key partners in our new Cambridge residence; Boston-Cambridge big pharma and biotech, members of the venture capital community, renowned researchers, advocacy groups and Pfizer Cambridge scientists and clinicians.

Boston/Cambridge is one of most prominent biomedical hubs in the world and known for its thriving economy. Recent advances in biomedical innovation and cutting-edge technologies have been a major factor in stimulating growth for the city. The close proximity of big pharma, biotech, academia and venture capital in Boston/Cambridge has particularly been crucial in fostering a culture ripe for such innovation.

Bruce Katz will shed light on the state of the local and global economy and the role innovation districts can play in accelerating therapies to patients. Katz will focus on the success Boston/Cambridge has had thus far in advancing biomedical discoveries as well as offer insights on the city’s future outlook.

The Brookings Institution is a nonprofit public policy organization based in Washington, D.C. Mr. Katz is Founding Director of the Brookings Metropolitan Policy Program, which aims to provide decision makers in the public, corporate, and civic sectors with policy ideas for improving the health and prosperity of cities and metropolitan areas.

Agenda:

5:30-6PM Registration/Gathering (please arrive by no later than 5:45PM EDT with a
government issued ID to allow sufficient time for security check)

6-7PM Welcoming remarks by Cambridge/Boston Site Head and Group Senior
Vice-President WorldWide R&D, Dr. Jose-Carlos Gutierrez-Ramos

                        Keynote speaker: Bruce Katz,
                        Founding Director Metropolitan Policy Program
                        Vice-president, The Brookings Institution

7-8PM Open reception and Networking

8PM Event ends

This May, Pfizer Cambridge sites are integrating and relocating our research and development teams into our new local headquarters at 610 Main Street, Cambridge, MA 02139. The unified Cambridge presence represents the opportunity to interlace Pfizer’s R&D capability in the densest biomedical community in the world, to potentially expand our already existing collaborations and to embark on forging possible new connections. These events will further drive our collective mission and passion to deliver new medicines to patients in need. Our distinguished invited guests will include leaders in the Boston-Cambridge venture capital and biotech community, renowned researchers, advocacy groups and Pfizer Cambridge scientists and clinicians.

Online registration:
If you are experiencing issues with online registration, please contact: Cambridge_site_head@pfizer.com

Industry:	Diversified FInancials/Private Equity/Venture Capital/Angel Funding Health Care Equipment & Services Pharmaceuticals/Biotechnology (Biotech)/Life Sciences
Issues:	Economic Issues Innovation
Target Audience:	Private Investors

Hashtags: #bcnet-PCCIE

Monday, September 8 2014 5:30pm – 7:00pm Other Time

Location: Pfizer Inc.
610 Main St
Cambridge, MA 02139

Contact:

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Proteomics, Metabolomics, Signaling Pathways, and Cell Regulation: a Compilation of Articles in the Journal http://pharmaceuticalintelligence.com

Posted in Biological Networks, Biomarkers & Medical Diagnostics, Biomedical Measurement Science, Calcium Signaling, CANCER BIOLOGY & Innovations in Cancer Therapy, Cardiovascular Research, Cell Biology, Chemical Biology and its relations to Metabolic Disease, Chemical Genetics, Coagulation Therapy and Internal Bleeding, Diabetes Mellitus, Disease Biology, FDA Regulatory Affairs, Frontiers in Cardiology and Cardiovascular Disorders, Gene Regulation and Evolution, Genetics & Pharmaceutical, Genome Biology, Genomic Expression, Genomic Testing: Methodology for Diagnosis, Infectious Disease & New Antibiotic Targets, Innovation in Immunology Diagnostics, Lipid metabolism, Liver & Digestive Diseases Research, Metabolomics, Molecular Genetics & Pharmaceutical, Myocardial adenine nucleotide metabolism, Myocardial Ischemia, Myocardial Metabolism, Nitric Oxide in Health and Disease, Nutritional Supplements: Atherogenesis, Pharmacotherapy and Cell Activity, Pharmacotherapy of Cardiovascular Disease, Population Health Management, Proteomics, Signaling, Signaling & Cell Circuits, Small Molecules in Development of Therapeutic Drugs, Systemic Inflammatory Response Related Disorders, Translational Research, Translational Science, tagged Alzheimers Disease, Apoptosis, Aviva Lev-Ari, bibliorgaphy, Biochemistry and Molecular Biology, biomarkers, breast cancer, Cancer research, Cardiovascular disease, Chemotherapy, compilation, Conditions and Diseases, curations, Diabetes mellitus type 2, DNA, Endothelium, gene, gene expression, Genome-wide association study, Human Genome Project, immune system, Leaders in Pharmaceutical Intelligence, Messenger RNA, Metabolism, Metabolomics, metastasis, MicroRNA, mitochondria, National Human Genome Research Institute, National Institutes of Health, Nitric oxide synthase, NO, Personalized medicine, Proceedings of the National Academy of Sciences of the United States of America, Proteomics, RNA, Signal transduction, Single-nucleotide polymorphism, Stanford University, Stem cell, Warburg Effect on September 1, 2014| Leave a Comment »

Compilation of References by Leaders in Pharmaceutical Business Intelligence in the Journal http://pharmaceuticalintelligence.com about
Proteomics, Metabolomics, Signaling Pathways, and Cell Regulation

Curator: Larry H Bernstein, MD, FCAP

Proteomics

The Human Proteome Map Completed

Reporter and Curator: Larry H. Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2014/08/28/the-human-proteome-map-completed/

Proteomics – The Pathway to Understanding and Decision-making in Medicine

Author and Curator, Larry H Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2014/06/24/proteomics-the-pathway-to-
understanding-and-decision-making-in-medicine/

3. Advances in Separations Technology for the “OMICs” and Clarification of Therapeutic Targets

Author and Curator, Larry H Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2012/10/22/advances-in-separations-technology-for-the-omics-and-clarification- of-therapeutic-targets/

Expanding the Genetic Alphabet and Linking the Genome to the Metabolome

Author and Curator, Larry H Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2012/09/24/expanding-the-genetic-alphabet-and-linking-the-genome-to-the- metabolome/

5. Genomics, Proteomics and standards

Larry H Bernstein, MD, FCAP, Author and Curator

http://pharmaceuticalintelligence.com/2014/07/06/genomics-proteomics-and-standards/

6. Proteins and cellular adaptation to stress

Larry H Bernstein, MD, FCAP, Author and Curator

http://pharmaceuticalintelligence.com/2014/07/08/proteins-and-cellular-adaptation-to-stress/

Metabolomics

Extracellular evaluation of intracellular flux in yeast cells

Larry H. Bernstein, MD, FCAP, Reviewer and Curator

http://pharmaceuticalintelligence.com/2014/08/25/extracellular-evaluation-of-intracellular-flux-in-yeast-cells/

Metabolomic analysis of two leukemia cell lines. I.

Larry H. Bernstein, MD, FCAP, Reviewer and Curator

http://pharmaceuticalintelligence.com/2014/08/23/metabolomic-analysis-of-two-leukemia-cell-lines-_i/

Metabolomic analysis of two leukemia cell lines. II.

Larry H. Bernstein, MD, FCAP, Reviewer and Curator

http://pharmaceuticalintelligence.com/2014/08/24/metabolomic-analysis-of-two-leukemia-cell-lines-ii/

Metabolomics, Metabonomics and Functional Nutrition: the next step in nutritional metabolism and biotherapeutics

Reviewer and Curator, Larry H. Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2014/08/22/metabolomics-metabonomics-and-functional-nutrition-the-next-step- in-nutritional-metabolism-and-biotherapeutics/

Buffering of genetic modules involved in tricarboxylic acid cycle metabolism provides homeomeostatic regulation

Larry H. Bernstein, MD, FCAP, Reviewer and curator

http://pharmaceuticalintelligence.com/2014/08/27/buffering-of-genetic-modules-involved-in-tricarboxylic-acid-cycle- metabolism-provides-homeomeostatic-regulation/

Metabolic Pathways

Pentose Shunt, Electron Transfer, Galactose, more Lipids in brief

Reviewer and Curator: Larry H. Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2014/08/21/pentose-shunt-electron-transfer-galactose-more-lipids-in-brief/

Mitochondria: More than just the “powerhouse of the cell”

Ritu Saxena, PhD

http://pharmaceuticalintelligence.com/2012/07/09/mitochondria-more-than-just-the-powerhouse-of-the-cell/

Mitochondrial fission and fusion: potential therapeutic targets?

Ritu saxena

http://pharmaceuticalintelligence.com/2012/10/31/mitochondrial-fission-and-fusion-potential-therapeutic-target/

4. Mitochondrial mutation analysis might be “1-step” away

Ritu Saxena

http://pharmaceuticalintelligence.com/2012/08/14/mitochondrial-mutation-analysis-might-be-1-step-away/

Selected References to Signaling and Metabolic Pathways in PharmaceuticalIntelligence.com

Curator: Larry H. Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2014/08/14/selected-references-to-signaling-and-metabolic-pathways-in- leaders-in-pharmaceutical-intelligence/

Metabolic drivers in aggressive brain tumors

Prabodh Kandal, PhD

http://pharmaceuticalintelligence.com/2012/11/11/metabolic-drivers-in-aggressive-brain-tumors/

Metabolite Identification Combining Genetic and Metabolic Information: Genetic association links unknown metabolites to functionally related genes

Writer and Curator, Aviva Lev-Ari, PhD, RD

http://pharmaceuticalintelligence.com/2012/10/22/metabolite-identification-combining-genetic-and-metabolic- information-genetic-association-links-unknown-metabolites-to-functionally-related-genes/

Mitochondria: Origin from oxygen free environment, role in aerobic glycolysis, metabolic adaptation

Larry H Bernstein, MD, FCAP, author and curator

http://pharmaceuticalintelligence.com/2012/09/26/mitochondria-origin-from-oxygen-free-environment-role-in-aerobic- glycolysis-metabolic-adaptation/

Therapeutic Targets for Diabetes and Related Metabolic Disorders

Reporter, Aviva Lev-Ari, PhD, RD

http://pharmaceuticalintelligence.com/2012/08/20/therapeutic-targets-for-diabetes-and-related-metabolic-disorders/

10. Buffering of genetic modules involved in tricarboxylic acid cycle metabolism provides homeomeostatic regulation

Larry H. Bernstein, MD, FCAP, Reviewer and curator

http://pharmaceuticalintelligence.com/2014/08/27/buffering-of-genetic-modules-involved-in-tricarboxylic-acid-cycle- metabolism-provides-homeomeostatic-regulation/

11. The multi-step transfer of phosphate bond and hydrogen exchange energy

Larry H. Bernstein, MD, FCAP, Curator:

http://pharmaceuticalintelligence.com/2014/08/19/the-multi-step-transfer-of-phosphate-bond-and-hydrogen- exchange-energy/

12. Studies of Respiration Lead to Acetyl CoA

http://pharmaceuticalintelligence.com/2014/08/18/studies-of-respiration-lead-to-acetyl-coa/

13. Lipid Metabolism

Author and Curator: Larry H. Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2014/08/15/lipid-metabolism/

14. Carbohydrate Metabolism

Author and Curator: Larry H. Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2014/08/13/carbohydrate-metabolism/

15. Update on mitochondrial function, respiration, and associated disorders

Larry H. Bernstein, MD, FCAP, Author and Curator

http://pharmaceuticalintelligence.com/2014/07/08/update-on-mitochondrial-function-respiration-and-associated- disorders/

16. Prologue to Cancer – e-book Volume One – Where are we in this journey?

Author and Curator: Larry H. Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2014/04/13/prologue-to-cancer-ebook-4-where-are-we-in-this-journey/

17. Introduction – The Evolution of Cancer Therapy and Cancer Research: How We Got Here?

Author and Curator: Larry H. Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2014/04/04/introduction-the-evolution-of-cancer-therapy-and-cancer-research- how-we-got-here/

18. Inhibition of the Cardiomyocyte-Specific Kinase TNNI3K

Author and Curator: Larry H. Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2013/11/01/inhibition-of-the-cardiomyocyte-specific-kinase-tnni3k/

19. The Binding of Oligonucleotides in DNA and 3-D Lattice Structures

Author and Curator: Larry H. Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2013/05/15/the-binding-of-oligonucleotides-in-dna-and-3-d-lattice-structures/

20. Mitochondrial Metabolism and Cardiac Function

Author and Curator: Larry H. Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2013/04/14/mitochondrial-metabolism-and-cardiac-function/

21. How Methionine Imbalance with Sulfur-Insufficiency Leads to Hyperhomocysteinemia

Curator: Larry H. Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2013/04/04/sulfur-deficiency-leads_to_hyperhomocysteinemia/

22. AMPK Is a Negative Regulator of the Warburg Effect and Suppresses Tumor Growth In Vivo

Author and Curator: Stephen J. Williams, PhD

http://pharmaceuticalintelligence.com/2013/03/12/ampk-is-a-negative-regulator-of-the-warburg-effect-and-suppresses- tumor-growth-in-vivo/

23. A Second Look at the Transthyretin Nutrition Inflammatory Conundrum

Author and Curator: Larry H. Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2012/12/03/a-second-look-at-the-transthyretin-nutrition-inflammatory- conundrum/

24. Mitochondrial Damage and Repair under Oxidative Stress

Author and Curator: Larry H. Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2012/10/28/mitochondrial-damage-and-repair-under-oxidative-stress/

25. Nitric Oxide and Immune Responses: Part 2

Author and Curator: Aviral Vatsa, PhD, MBBS

http://pharmaceuticalintelligence.com/2012/10/28/nitric-oxide-and-immune-responses-part-2/

26. Overview of Posttranslational Modification (PTM)

Writer and Curator: Larry H. Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2014/07/29/overview-of-posttranslational-modification-ptm/

27. Malnutrition in India, high newborn death rate and stunting of children age under five years

Writer and Curator: Larry H. Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2014/07/15/malnutrition-in-india-high-newborn-death-rate-and-stunting-of- children-age-under-five-years/

28. Update on mitochondrial function, respiration, and associated disorders

Writer and Curator: Larry H. Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2014/07/08/update-on-mitochondrial-function-respiration-and-associated- disorders/

29. Omega-3 fatty acids, depleting the source, and protein insufficiency in renal disease

Larry H. Bernstein, MD, FCAP, Curator

http://pharmaceuticalintelligence.com/2014/07/06/omega-3-fatty-acids-depleting-the-source-and-protein-insufficiency- in-renal-disease/

30. Introduction to e-Series A: Cardiovascular Diseases, Volume Four Part 2: Regenerative Medicine

Larry H. Bernstein, MD, FCAP, writer, and Aviva Lev- Ari, PhD, RN

http://pharmaceuticalintelligence.com/2014/04/27/larryhbernintroduction_to_cardiovascular_diseases- translational_medicine-part_2/

31. Epilogue: Envisioning New Insights in Cancer Translational Biology
Series C: e-Books on Cancer & Oncology

Author & Curator: Larry H. Bernstein, MD, FCAP, Series C Content Consultant

http://pharmaceuticalintelligence.com/2014/03/29/epilogue-envisioning-new-insights/

32. Ca2+-Stimulated Exocytosis: The Role of Calmodulin and Protein Kinase C in Ca2+ Regulation of Hormone and Neurotransmitter

Writer and Curator: Larry H Bernstein, MD, FCAP and
Curator and Content Editor: Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2013/12/23/calmodulin-and-protein-kinase-c-drive-the-ca2-regulation-of- hormone-and-neurotransmitter-release-that-triggers-ca2-stimulated-exocy

33. Cardiac Contractility & Myocardial Performance: Therapeutic Implications of Ryanopathy (Calcium Release- related Contractile Dysfunction) and Catecholamine Responses

Author, and Content Consultant to e-SERIES A: Cardiovascular Diseases: Justin Pearlman, MD, PhD, FACC
Author and Curator: Larry H Bernstein, MD, FCAP
and Article Curator: Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2013/08/28/cardiac-contractility-myocardium-performance-ventricular-arrhythmias- and-non-ischemic-heart-failure-therapeutic-implications-for-cardiomyocyte-ryanopathy-calcium-release-related- contractile/

34. Role of Calcium, the Actin Skeleton, and Lipid Structures in Signaling and Cell Motility

Author and Curator: Larry H Bernstein, MD, FCAP Author: Stephen Williams, PhD, and Curator: Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2013/08/26/role-of-calcium-the-actin-skeleton-and-lipid-structures-in-signaling-and-cell-motility/

35. Identification of Biomarkers that are Related to the Actin Cytoskeleton

Larry H Bernstein, MD, FCAP, Author and Curator

http://pharmaceuticalintelligence.com/2012/12/10/identification-of-biomarkers-that-are-related-to-the-actin- cytoskeleton/

36. Advanced Topics in Sepsis and the Cardiovascular System at its End Stage

Author: Larry H Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2013/08/18/advanced-topics-in-Sepsis-and-the-Cardiovascular-System-at-its- End-Stage/

37. The Delicate Connection: IDO (Indolamine 2, 3 dehydrogenase) and Cancer Immunology

Demet Sag, PhD, Author and Curator

http://pharmaceuticalintelligence.com/2013/08/04/the-delicate-connection-ido-indolamine-2-3-dehydrogenase-and- immunology/

38. IDO for Commitment of a Life Time: The Origins and Mechanisms of IDO, indolamine 2, 3-dioxygenase

Demet Sag, PhD, Author and Curator

http://pharmaceuticalintelligence.com/2013/08/04/ido-for-commitment-of-a-life-time-the-origins-and-mechanisms-of- ido-indolamine-2-3-dioxygenase/

39. Confined Indolamine 2, 3 dioxygenase (IDO) Controls the Homeostasis of Immune Responses for Good and Bad

Curator: Demet Sag, PhD, CRA, GCP

http://pharmaceuticalintelligence.com/2013/07/31/confined-indolamine-2-3-dehydrogenase-controls-the-hemostasis- of-immune-responses-for-good-and-bad/

40. Signaling Pathway that Makes Young Neurons Connect was discovered @ Scripps Research Institute

Reporter: Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2013/06/26/signaling-pathway-that-makes-young-neurons-connect-was- discovered-scripps-research-institute/

41. Naked Mole Rats Cancer-Free

Writer and Curator: Larry H. Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2013/06/20/naked-mole-rats-cancer-free/

42. Late Onset of Alzheimer’s Disease and One-carbon Metabolism

Reporter and Curator: Dr. Sudipta Saha, Ph.D.

http://pharmaceuticalintelligence.com/2013/05/06/alzheimers-disease-and-one-carbon-metabolism/

43. Problems of vegetarianism

Reporter and Curator: Dr. Sudipta Saha, Ph.D.

http://pharmaceuticalintelligence.com/2013/04/22/problems-of-vegetarianism/

44. Amyloidosis with Cardiomyopathy

Writer and Curator: Larry H. Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2013/03/31/amyloidosis-with-cardiomyopathy/

45. Liver endoplasmic reticulum stress and hepatosteatosis

Larry H Bernstein, MD, FACP

http://pharmaceuticalintelligence.com/2013/03/10/liver-endoplasmic-reticulum-stress-and-hepatosteatosis/

46. The Molecular Biology of Renal Disorders: Nitric Oxide – Part III

Curator and Author: Larry H Bernstein, MD, FACP

http://pharmaceuticalintelligence.com/2012/11/26/the-molecular-biology-of-renal-disorders/

47. Nitric Oxide Function in Coagulation – Part II

Curator and Author: Larry H. Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2012/11/26/nitric-oxide-function-in-coagulation/

48. Nitric Oxide, Platelets, Endothelium and Hemostasis

Curator and Author: Larry H Bernstein, MD, FACP

http://pharmaceuticalintelligence.com/2012/11/08/nitric-oxide-platelets-endothelium-and-hemostasis/

49. Interaction of Nitric Oxide and Prostacyclin in Vascular Endothelium

Curator and Author: Larry H Bernstein, MD, FACP

http://pharmaceuticalintelligence.com/2012/09/14/interaction-of-nitric-oxide-and-prostacyclin-in-vascular-endothelium/

50. Nitric Oxide and Immune Responses: Part 1

Curator and Author: Aviral Vatsa PhD, MBBS

http://pharmaceuticalintelligence.com/2012/10/18/nitric-oxide-and-immune-responses-part-1/

51. Nitric Oxide and Immune Responses: Part 2

Curator and Author: Aviral Vatsa PhD, MBBS

http://pharmaceuticalintelligence.com/2012/10/28/nitric-oxide-and-immune-responses-part-2/

52. Mitochondrial Damage and Repair under Oxidative Stress

Curator and Author: Larry H Bernstein, MD, FACP

http://pharmaceuticalintelligence.com/2012/10/28/mitochondrial-damage-and-repair-under-oxidative-stress/

53. Is the Warburg Effect the cause or the effect of cancer: A 21st Century View?

Curator and Author: Larry H Bernstein, MD, FACP

http://pharmaceuticalintelligence.com/2012/10/17/is-the-warburg-effect-the-cause-or-the-effect-of-cancer-a-21st- century-view/

54. Ubiquinin-Proteosome pathway, autophagy, the mitochondrion, proteolysis and cell apoptosis

Curator and Author: Larry H Bernstein, MD, FACP

http://pharmaceuticalintelligence.com/2012/10/30/ubiquinin-proteosome-pathway-autophagy-the-mitochondrion- proteolysis-and-cell-apoptosis/

55. Ubiquitin-Proteosome pathway, Autophagy, the Mitochondrion, Proteolysis and Cell Apoptosis: Part III

Curator and Author: Larry H Bernstein, MD, FACP

http://pharmaceuticalintelligence.com/2013/02/14/ubiquinin-proteosome-pathway-autophagy-the-mitochondrion- proteolysis-and-cell-apoptosis-reconsidered/

56. Nitric Oxide and iNOS have Key Roles in Kidney Diseases – Part II

Curator and Author: Larry H Bernstein, MD, FACP

http://pharmaceuticalintelligence.com/2012/11/26/nitric-oxide-and-inos-have-key-roles-in-kidney-diseases/

57. New Insights on Nitric Oxide donors – Part IV

Curator and Author: Larry H Bernstein, MD, FACP

http://pharmaceuticalintelligence.com/2012/11/26/new-insights-on-no-donors/

58. Crucial role of Nitric Oxide in Cancer

Curator and Author: Ritu Saxena, Ph.D.

http://pharmaceuticalintelligence.com/2012/10/16/crucial-role-of-nitric-oxide-in-cancer/

59. Nitric Oxide has a ubiquitous role in the regulation of glycolysis -with a concomitant influence on mitochondrial function

Curator and Author: Larry H Bernstein, MD, FACP

http://pharmaceuticalintelligence.com/2012/09/16/nitric-oxide-has-a-ubiquitous-role-in-the-regulation-of-glycolysis-with- a-concomitant-influence-on-mitochondrial-function/

60. Targeting Mitochondrial-bound Hexokinase for Cancer Therapy

Curator and Author: Ziv Raviv, PhD, RN 04/06/2013

http://pharmaceuticalintelligence.com/2013/04/06/targeting-mitochondrial-bound-hexokinase-for-cancer-therapy/

61. Biochemistry of the Coagulation Cascade and Platelet Aggregation – Part I

Curator and Author: Larry H Bernstein, MD, FACP

http://pharmaceuticalintelligence.com/2012/11/26/biochemistry-of-the-coagulation-cascade-and-platelet-aggregation/

Genomics, Transcriptomics, and Epigenetics

What is the meaning of so many RNAs?

Writer and Curator: Larry H. Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2014/08/06/what-is-the-meaning-of-so-many-rnas/

RNA and the transcription the genetic code

Larry H. Bernstein, MD, FCAP, Writer and Curator

http://pharmaceuticalintelligence.com/2014/08/02/rna-and-the-transcription-of-the-genetic-code/

A Primer on DNA and DNA Replication

Writer and Curator: Larry H. Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2014/07/29/a_primer_on_dna_and_dna_replication/

4. Synthesizing Synthetic Biology: PLOS Collections

Reporter: Aviva Lev-Ari

http://pharmaceuticalintelligence.com/2012/08/17/synthesizing-synthetic-biology-plos-collections/

5. Pathology Emergence in the 21st Century

Author and Curator: Larry Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2014/08/03/pathology-emergence-in-the-21st-century/

6. RNA and the transcription the genetic code

Writer and Curator, Larry H. Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2014/08/02/rna-and-the-transcription-of-the-genetic-code/

7. A Great University engaged in Drug Discovery: University of Pittsburgh

Larry H. Bernstein, MD, FCAP, Reporter and Curator

http://pharmaceuticalintelligence.com/2014/07/15/a-great-university-engaged-in-drug-discovery/

8. microRNA called miRNA-142 involved in the process by which the immature cells in the bone marrow give rise to all the types of blood cells, including immune cells and the oxygen-bearing red blood cells

Aviva Lev-Ari, PhD, RN, Author and Curator

http://pharmaceuticalintelligence.com/2014/07/24/microrna-called-mir-142-involved-in-the-process-by-which-the- immature-cells-in-the-bone-marrow-give-rise-to-all-the-types-of-blood-cells-including-immune-cells-and-the-oxygen- bearing-red-blood-cells/

9. Genes, proteomes, and their interaction

Larry H. Bernstein, MD, FCAP, Writer and Curator

http://pharmaceuticalintelligence.com/2014/07/28/genes-proteomes-and-their-interaction/

10. Regulation of somatic stem cell Function

Larry H. Bernstein, MD, FCAP, Writer and Curator Aviva Lev-Ari, PhD, RN, Curator

http://pharmaceuticalintelligence.com/2014/07/29/regulation-of-somatic-stem-cell-function/

11. Scientists discover that pluripotency factor NANOG is also active in adult organisms

Larry H. Bernstein, MD, FCAP, Reporter

http://pharmaceuticalintelligence.com/2014/07/10/scientists-discover-that-pluripotency-factor-nanog-is-also-active-in- adult-organisms/

12. Bzzz! Are fruitflies like us?

Larry H Bernstein, MD, FCAP, Author and Curator

http://pharmaceuticalintelligence.com/2014/07/07/bzzz-are-fruitflies-like-us/

13. Long Non-coding RNAs Can Encode Proteins After All

Larry H Bernstein, MD, FCAP, Reporter

http://pharmaceuticalintelligence.com/2014/06/29/long-non-coding-rnas-can-encode-proteins-after-all/

14. Michael Snyder @Stanford University sequenced the lymphoblastoid transcriptomes and developed an
allele-specific full-length transcriptome

Aviva Lev-Ari, PhD, RN, Author and Curator

http://pharmaceuticalintelligence.com/014/06/23/michael-snyder-stanford-university-sequenced-the-lymphoblastoid- transcriptomes-and-developed-an-allele-specific-full-length-transcriptome/

15. Commentary on Biomarkers for Genetics and Genomics of Cardiovascular Disease: Views by Larry H Bernstein, MD, FCAP

Author: Larry H Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2014/07/16/commentary-on-biomarkers-for-genetics-and-genomics-of- cardiovascular-disease-views-by-larry-h-bernstein-md-fcap/

16. Observations on Finding the Genetic Links in Common Disease: Whole Genomic Sequencing Studies

Author an curator: Larry H Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2013/05/18/observations-on-finding-the-genetic-links/

17. Silencing Cancers with Synthetic siRNAs

Larry H. Bernstein, MD, FCAP, Reviewer and Curator

http://pharmaceuticalintelligence.com/2013/12/09/silencing-cancers-with-synthetic-sirnas/

18. Cardiometabolic Syndrome and the Genetics of Hypertension: The Neuroendocrine Transcriptome Control Points

Reporter: Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2013/12/12/cardiometabolic-syndrome-and-the-genetics-of-hypertension-the-neuroendocrine-transcriptome-control-points/

19. Developments in the Genomics and Proteomics of Type 2 Diabetes Mellitus and Treatment Targets

Larry H. Bernstein, MD, FCAP, Reviewer and Curator

http://pharmaceuticalintelligence.com/2013/12/08/developments-in-the-genomics-and-proteomics-of-type-2-diabetes- mellitus-and-treatment-targets/

20. Loss of normal growth regulation

Larry H Bernstein, MD, FCAP, Curator

http://pharmaceuticalintelligence.com/2014/07/06/loss-of-normal-growth-regulation/

21. CT Angiography & TrueVision™ Metabolomics (Genomic Phenotyping) for new Therapeutic Targets to Atherosclerosis

Reporter: Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2013/11/15/ct-angiography-truevision-metabolomics-genomic-phenotyping-for- new-therapeutic-targets-to-atherosclerosis/

22. CRACKING THE CODE OF HUMAN LIFE: The Birth of BioInformatics & Computational Genomics

Genomics Curator, Larry H Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2014/08/30/cracking-the-code-of-human-life-the-birth-of-bioinformatics- computational-genomics/

23. Big Data in Genomic Medicine

Author and Curator, Larry H Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2012/12/17/big-data-in-genomic-medicine/

24. From Genomics of Microorganisms to Translational Medicine

Author and Curator: Demet Sag, PhD

http://pharmaceuticalintelligence.com/2014/03/20/without-the-past-no-future-but-learn-and-move-genomics-of- microorganisms-to-translational-medicine/

25. Summary of Genomics and Medicine: Role in Cardiovascular Diseases

Author and Curator, Larry H Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2014/01/06/summary-of-genomics-and-medicine-role-in-cardiovascular-diseases/

26. Genomic Promise for Neurodegenerative Diseases, Dementias, Autism Spectrum, Schizophrenia, and Serious Depression

Author and Curator, Larry H Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2013/02/19/genomic-promise-for-neurodegenerative-diseases-dementias-autism- spectrum-schizophrenia-and-serious-depression/

27. BRCA1 a tumour suppressor in breast and ovarian cancer – functions in transcription, ubiquitination and DNA repair

Sudipta Saha, PhD

http://pharmaceuticalintelligence.com/2012/12/04/brca1-a-tumour-suppressor-in-breast-and-ovarian-cancer-functions- in-transcription-ubiquitination-and-dna-repair/

28. Personalized medicine gearing up to tackle cancer

Ritu Saxena, PhD

http://pharmaceuticalintelligence.com/2013/01/07/personalized-medicine-gearing-up-to-tackle-cancer/

29. Differentiation Therapy – Epigenetics Tackles Solid Tumors

Stephen J Williams, PhD

http://pharmaceuticalintelligence.com/2013/01/03/differentiation-therapy-epigenetics-tackles-solid-tumors/

30. Mechanism involved in Breast Cancer Cell Growth: Function in Early Detection & Treatment

Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2013/01/17/mechanism-involved-in-breast-cancer-cell-growth-function-in-early- detection-treatment/

31. The Molecular pathology of Breast Cancer Progression

Tilde Barliya, PhD

http://pharmaceuticalintelligence.com/2013/01/10/the-molecular-pathology-of-breast-cancer-progression

32. Gastric Cancer: Whole-genome reconstruction and mutational signatures

Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2012/12/24/gastric-cancer-whole-genome-reconstruction-and-mutational- signatures-2/

33. Paradigm Shift in Human Genomics – Predictive Biomarkers and Personalized Medicine – Part 1 (pharmaceuticalintelligence.com)

Aviva Lev-Ari, PhD, RN

http://pharmaceuticalntelligence.com/2013/01/13/paradigm-shift-in-human-genomics-predictive-biomarkers-and-personalized-medicine-part-1/

34. LEADERS in Genome Sequencing of Genetic Mutations for Therapeutic Drug Selection in Cancer Personalized Treatment: Part 2

A Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2013/01/13/leaders-in-genome-sequencing-of-genetic-mutations-for-therapeutic- drug-selection-in-cancer-personalized-treatment-part-2/

35. Personalized Medicine: An Institute Profile – Coriell Institute for Medical Research: Part 3

Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2013/01/13/personalized-medicine-an-institute-profile-coriell-institute-for-medical- research-part-3/

36. Harnessing Personalized Medicine for Cancer Management, Prospects of Prevention and Cure: Opinions of Cancer Scientific Leaders @http://pharmaceuticalintelligence.com

Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2013/01/13/7000/Harnessing_Personalized_Medicine_for_ Cancer_Management- Prospects_of_Prevention_and_Cure/

37. GSK for Personalized Medicine using Cancer Drugs needs Alacris systems biology model to determine the in silico
effect of the inhibitor in its “virtual clinical trial”

Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2012/11/14/gsk-for-personalized-medicine-using-cancer-drugs-needs-alacris- systems-biology-model-to-determine-the-in-silico-effect-of-the-inhibitor-in-its-virtual-clinical-trial/

38. Personalized medicine-based cure for cancer might not be far away

Ritu Saxena, PhD

http://pharmaceuticalintelligence.com/2012/11/20/personalized-medicine-based-cure-for-cancer-might-not-be-far-away/

39. Human Variome Project: encyclopedic catalog of sequence variants indexed to the human genome sequence

Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2012/11/24/human-variome-project-encyclopedic-catalog-of-sequence-variants- indexed-to-the-human-genome-sequence/

40. Inspiration From Dr. Maureen Cronin’s Achievements in Applying Genomic Sequencing to Cancer Diagnostics

Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2013/01/10/inspiration-from-dr-maureen-cronins-achievements-in-applying- genomic-sequencing-to-cancer-diagnostics/

41. The “Cancer establishments” examined by James Watson, co-discoverer of DNA w/Crick, 4/1953

Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2013/01/09/the-cancer-establishments-examined-by-james-watson-co-discover- of-dna-wcrick-41953/

42. What can we expect of tumor therapeutic response?

Author and curator: Larry H Bernstein, MD, FACP

http://pharmaceuticalintelligence.com/2012/12/05/what-can-we-expect-of-tumor-therapeutic-response/

43. Directions for genomics in personalized medicine

Author and Curator: Larry H. Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2013/01/27/directions-for-genomics-in-personalized-medicine/

44. How mobile elements in “Junk” DNA promote cancer. Part 1: Transposon-mediated tumorigenesis.

Stephen J Williams, PhD

http://pharmaceuticalintelligence.com/2012/10/31/how-mobile-elements-in-junk-dna-prote-cancer-part1-transposon- mediated-tumorigenesis/

45. mRNA interference with cancer expression

Author and Curator, Larry H. Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2012/10/26/mrna-interference-with-cancer-expression/

46. Expanding the Genetic Alphabet and linking the genome to the metabolome

Aviva Lev-Ari, PhD, RD

http://pharmaceuticalintelligence.com/2012/09/24/expanding-the-genetic-alphabet-and-linking-the-genome-to-the- metabolome/

47. Breast Cancer, drug resistance, and biopharmaceutical targets

Author and Curator: Larry H Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2012/09/18/breast-cancer-drug-resistance-and-biopharmaceutical-targets/

48. Breast Cancer: Genomic profiling to predict Survival: Combination of Histopathology and Gene Expression Analysis

Aviva Lev-Ari, PhD, RD

http://pharmaceuticalintelligence.com/2012/12/24/breast-cancer-genomic-profiling-to-predict-survival-combination-of- histopathology-and-gene-expression-analysis

49. Gastric Cancer: Whole-genome reconstruction and mutational signatures

Aviva Lev-Ari, PhD, RD

http://pharmaceuticalintelligence.com/2012/12/24/gastric-cancer-whole-genome-reconstruction-and-mutational- signatures-2/

50. Genomic Analysis: FLUIDIGM Technology in the Life Science and Agricultural Biotechnology

Aviva Lev-Ari, PhD, RD

http://pharmaceuticalintelligence.com/2012/08/22/genomic-analysis-fluidigm-technology-in-the-life-science-and- agricultural-biotechnology/

51. 2013 Genomics: The Era Beyond the Sequencing Human Genome: Francis Collins, Craig Venter, Eric Lander, et al.

Aviva Lev-Ari, PhD, RD

http://pharmaceuticalintelligence.com/2013_Genomics

52. Paradigm Shift in Human Genomics – Predictive Biomarkers and Personalized Medicine – Part 1

Aviva Lev-Ari, PhD, RD

http://pharmaceuticalintelligence.com/Paradigm Shift in Human Genomics_/

Signaling Pathways

Proteins and cellular adaptation to stress

Larry H Bernstein, MD, FCAP, Curator

http://pharmaceuticalintelligence.com/2014/07/08/proteins-and-cellular-adaptation-to-stress/

A Synthesis of the Beauty and Complexity of How We View Cancer:
Cancer Volume One – Summary

Author and Curator: Larry H. Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2014/03/26/a-synthesis-of-the-beauty-and-complexity-of-how-we-view-cancer/

Recurrent somatic mutations in chromatin-remodeling and ubiquitin ligase complex genes in
serous endometrial tumors

Sudipta Saha, PhD

http://pharmaceuticalintelligence.com/2012/11/19/recurrent-somatic-mutations-in-chromatin-remodeling-ad-ubiquitin- ligase-complex-genes-in-serous-endometrial-tumors/

4. Prostate Cancer Cells: Histone Deacetylase Inhibitors Induce Epithelial-to-Mesenchymal Transition

Stephen J Williams, PhD

http://pharmaceuticalintelligence.com/2012/11/30/histone-deacetylase-inhibitors-induce-epithelial-to-mesenchymal- transition-in-prostate-cancer-cells/

5. Ubiquinin-Proteosome pathway, autophagy, the mitochondrion, proteolysis and cell apoptosis

Author and Curator: Larry H Bernstein, MD, FCAP

http://pharmaceuticalintelligence.com/2012/10/30/ubiquinin-proteosome-pathway-autophagy-the-mitochondrion- proteolysis-and-cell-apoptosis/

6. Signaling and Signaling Pathways

Larry H. Bernstein, MD, FCAP, Reporter and Curator

http://pharmaceuticalintelligence.com/2014/08/12/signaling-and-signaling-pathways/

7. Leptin signaling in mediating the cardiac hypertrophy associated with obesity

Larry H. Bernstein, MD, FCAP, Reporter and Curator

http://pharmaceuticalintelligence.com/2013/11/03/leptin-signaling-in-mediating-the-cardiac-hypertrophy-associated- with-obesity/

Sensors and Signaling in Oxidative Stress

Larry H. Bernstein, MD, FCAP, Reporter and Curator

http://pharmaceuticalintelligence.com/2013/11/01/sensors-and-signaling-in-oxidative-stress/

The Final Considerations of the Role of Platelets and Platelet Endothelial Reactions in Atherosclerosis and Novel
Treatments

Larry H. Bernstein, MD, FCAP, Reporter and Curator

http://pharmaceuticalintelligence.com/2013/10/15/the-final-considerations-of-the-role-of-platelets-and-platelet- endothelial-reactions-in-atherosclerosis-and-novel-treatments

10. Platelets in Translational Research – Part 1

Larry H. Bernstein, MD, FCAP, Reporter and Curator

http://pharmaceuticalintelligence.com/2013/10/07/platelets-in-translational-research-1/

11. Disruption of Calcium Homeostasis: Cardiomyocytes and Vascular Smooth Muscle Cells: The Cardiac and
Cardiovascular Calcium Signaling Mechanism

Author and Curator: Larry H Bernstein, MD, FCAP, Author, and Content Consultant to e-SERIES A:
Cardiovascular Diseases: Justin Pearlman, MD, PhD, FACC and Curator: Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2013/09/12/disruption-of-calcium-homeostasis-cardiomyocytes-and-vascular- smooth-muscle-cells-the-cardiac-and-cardiovascular-calcium-signaling-mechanism/

12. The Centrality of Ca(2+) Signaling and Cytoskeleton Involving Calmodulin Kinases and
Ryanodine Receptors in Cardiac Failure, Arterial Smooth Muscle, Post-ischemic Arrhythmia,
Similarities and Differences, and Pharmaceutical Targets

Author and Curator: Larry H Bernstein, MD, FCAP, Author, and Content Consultant to
e-SERIES A: Cardiovascular Diseases: Justin Pearlman, MD, PhD, FACC and
Curator: Aviva Lev-Ari, PhD, RN

http://pharmaceuticalintelligence.com/2013/09/08/the-centrality-of-ca2-signaling-and-cytoskeleton-involving-calmodulin- kinases-and-ryanodine-receptors-in-cardiac-failure-arterial-smooth-muscle-post-ischemic-arrhythmia-similarities-and- differen/

13. Nitric Oxide Signalling Pathways

Aviral Vatsa, PhD, MBBS

http://pharmaceuticalintelligence.com/2012/08/22/nitric-oxide-signalling-pathways/

14. Immune activation, immunity, antibacterial activity

Larry H. Bernstein, MD, FCAP, Curator

http://pharmaceuticalintelligence.com/2014/07/06/immune-activation-immunity-antibacterial-activity/

15. Regulation of somatic stem cell Function

Larry H. Bernstein, MD, FCAP, Writer and Curator Aviva Lev-Ari, PhD, RN, Curator

http://pharmaceuticalintelligence.com/2014/07/29/regulation-of-somatic-stem-cell-function/

16. Scientists discover that pluripotency factor NANOG is also active in adult organisms

Larry H. Bernstein, MD, FCAP, Reporter

http://pharmaceuticalintelligence.com/2014/07/10/scientists-discover-that-pluripotency-factor-nanog-is-also-active-in-adult-organisms/

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Dompe’ Receives FDA orphan drug designation for rhNGF in the treatment of Neurotrophic Keratitis (NK).

Posted in Drug Delivery Platform Technology, FDA Regulatory Affairs, Molecular Genetics & Pharmaceutical, Pharmaceutical Drug Discovery, Pharmaceutical Industry Competitive Intelligence, Pharmaceutical R&D Investment, tagged Clinical trial, Clinical Trials, Conditions and Diseases, corneal, Dompe', FDA, FDA approval, Food and Drug Administration, neuortrophic keratitis, Ophthalmology, research, Retinitis Pignenotsa on July 24, 2014| Leave a Comment »

Dompe’ Receives FDA orphan drug designation for rhNGF in the treatment of Neurotrophic Keratitis (NK).

Reporter: Stephen J Williams, PhD

The U.S. FDA granted Dompe’ an orphan drug designation for rhNGF (recombinant human nerve growth factor) in the treatment of Neurotrophic Keratitis (NK).

Neurotrophic Keratitis (NK) is a rare, degenerative corneal disease caused by an impairment of corneal innervation (the distribution or supply of nerves), leading to a decrease or absence of corneal sensation and dysfunction of the corneal epithelium and abnormal corneal epithelial healing. The development of persistent epithelial defects or corneal ulcers can result in vision loss.

Severe NK is consistently recognized by clinicians as a serious condition lacking a highly effective treatment option.

The epidemiology of NK has not been well-defined. The estimated prevalence of patients with moderate-to-severe NK (stage 2-3) is less than 1 person in 5,000 globally.

Clinical trials in the U.S. are expected to begin in the next few months in leading research centers.

Dompé will be present at the American Association of Ophthalmology Annual meeting (Chicago, October 18-21). Currently, the enrollment is ongoing for the company’s Phase II trial with rhNGF in the treatment of NK.
Background – Dompé and its R&D

Dompé is a leading Italian biopharmaceutical company (with headquarters in Milan) committed to the development of innovative treatment solutions for rare, often orphan, diseases that have a high social impact, in areas where unmet treatment needs still exist.
The Company focuses its R&D activities in diabetes, ophthalmology, oncology and organ transplants.
The R&D activities are carried out in the Dompé biotech plant located in L’Aquila (Abruzzo), which has an internationally recognized expertise in the field of rare diseases.
This year (2014), Dompé opened an office in New York, staffed with scientists and R&D teams in order to carry out and coordinate the scientific activities in the U.S.

Dompé commitment in ophthalmology – rhNGF

In ophthalmology, Dompé is promoting the research and development of Nerve Growth Factor (NGF), a soluble protein that stimulates the growth, maintenance and survival of neurons, whose discovery led to Prof. Rita Levi Montalcini being awarded the Nobel Prize in 1986.
Recombinant human Nerve Growth Factor (rhNGF) has been studied and produced exclusively at Dompé’s production site in L’Aquila, Italy, and is undergoing an international Phase II trial, called “REPARO”, to evaluate its efficacy and safety in the treatment of Neurotrophic Keratitis, a rare orphan disease. The trial is being conducted in 39 centers and nine European countries.

The medicine recently has been designated an orphan drug for the treatment of Retinitis Pigmentosa (RP), a severe, genetic rare disease that can lead to blindness for which there is currently no treatment available. A clinical trial in the EU, involving patients with RP, started in the first quarter of 2014 with the enrolment of the first patient.

SOURCE

From: Gail Thornton <gailsthornton@yahoo.com>
Reply-To: Gail Thornton <gailsthornton@yahoo.com>
Date: Wed, 23 Jul 2014 07:02:05 -0700
To: Aviva Lev-Ari <avivalev-ari@alum.berkeley.edu>
Subject: Dompe’ Receives FDA orphan drug designation for rhNGF

Read Full Post »

Scientific Curation Fostering Expert Networks and Open Innovation: Lessons from Clive Thompson and others

Posted in Computational Biology/Systems and Bioinformatics, Curation, Curation methodology, Dialectic, Discovery process, Experimental validation, Explanatory, Health Economics and Outcomes Research, HealthCare IT, Open Access Journals, Pharmaceutical Industry Competitive Intelligence, Scientist: Career considerations, Scoop.it, Statistical Methods for Research Evaluation, Technology Advance Assessment of, Theoretic convergence, Uncategorized, tagged #science2_0, @science 2_0, Aviva Lev-Ari, collaboration, Conditions and Diseases, Content Curation, Curation, curation communities, Curation methodology, Curator, health, Larry H. Bernstein, medical literature, medical news, medical reporting, medicine, Open Access Online Scientific Journal, Open Access Publishing, Open data, science, Scientific literature, scientific networks, scientific news, Social network on July 17, 2014| Leave a Comment »

Scientific Curation Fostering Expert Networks and Open Innovation: Lessons from Clive Thompson

Curators and Writer: Stephen J. Williams, Ph.D. with input from Curators Larry H. Bernstein, MD, FCAP, Dr. Justin D. Pearlman, MD, PhD, FACC and Dr. Aviva Lev-Ari, PhD, RN

(this discussion is in a three part series including:

Using Scientific Content Curation as a Method for Validation and Biocuration

Using Scientific Content Curation as a Method for Open Innovation)

Every month I get my Wired Magazine (yes in hard print, I still like to turn pages manually plus I don’t mind if I get grease or wing sauce on my magazine rather than on my e-reader) but I always love reading articles written by Clive Thompson. He has a certain flair for understanding the techno world we live in and the human/technology interaction, writing about interesting ways in which we almost inadvertently integrate new technologies into our day-to-day living, generating new entrepreneurship, new value. He also writes extensively about tech and entrepreneurship.

October 2013 Wired article by Clive Thompson, entitled “How Successful Networks Nurture Good Ideas: Thinking Out Loud”, describes how the voluminous writings, postings, tweets, and sharing on social media is fostering connections between people and ideas which, previously, had not existed. The article was generated from Clive Thompson’s book Smarter Than you Think: How Technology is Changing Our Minds for the Better.Tom Peters also commented about the article in his blog (see here).

Clive gives a wonderful example of Ory Okolloh, a young Kenyan-born law student who, after becoming frustrated with the lack of coverage of problems back home, started a blog about Kenyan politics. Her blog not only got interest from movie producers who were documenting female bloggers but also gained the interest of fellow Kenyans who, during the upheaval after the 2007 Kenyan elections, helped Ory to develop a Google map for reporting of violence (http://www.ushahidi.com/, which eventually became a global organization using open-source technology to affect crises-management. There are a multitude of examples how networks and the conversations within these circles are fostering new ideas. As Clive states in the article:

Our ideas are PRODUCTS OF OUR ENVIRONMENT.

They are influenced by the conversations around us.

However the article got me thinking of how Science 2.0 and the internet is changing how scientists contribute, share, and make connections to produce new and transformative ideas.

But HOW MUCH Knowledge is OUT THERE?

Clive’s article listed some amazing facts about the mountains of posts, tweets, words etc. out on the internet EVERY DAY, all of which exemplifies the problem:

154.6 billion EMAILS per DAY
400 million TWEETS per DAY
1 million BLOG POSTS (including this one) per DAY
2 million COMMENTS on WordPress per DAY
16 million WORDS on Facebook per DAY
TOTAL 52 TRILLION WORDS per DAY

As he estimates this would be 520 million books per DAY (book with average 100,000 words).

A LOT of INFO. But as he suggests it is not the volume but how we create and share this information which is critical as the science fiction writer Theodore Sturgeon noted “Ninety percent of everything is crap” AKA Sturgeon’s Law.

Internet live stats show how congested the internet is each day (http://www.internetlivestats.com/). Needless to say Clive’s numbers are a bit off. As of the writing of this article:

2.9 billion internet users
981 million websites (only 25,000 hacked today)
128 billion emails
385 million Tweets
> 2.7 million BLOG posts today (including this one)

The Good, The Bad, and the Ugly of the Scientific Internet (The Wild West?)

So how many science blogs are out there? Well back in 2008 “grrlscientist” asked this question and turned up a total of 19,881 blogs however most were “pseudoscience” blogs, not written by Ph.D or MD level scientists. A deeper search on Technorati using the search term “scientist PhD” turned up about 2,000 written by trained scientists.

So granted, there is a lot of

….. when it comes to scientific information on the internet!

I had recently re-posted, on this site, a great example of how bad science and medicine can get propagated throughout the internet:

http://pharmaceuticalintelligence.com/2014/06/17/the-gonzalez-protocol-worse-than-useless-for-pancreatic-cancer/

and in a Nature Report:Stem cells: Taking a stand against pseudoscience

http://www.nature.com/news/stem-cells-taking-a-stand-against-pseudoscience-1.15408

Drs.Elena Cattaneo and Gilberto Corbellini document their long, hard fight against false and invalidated medical claims made by some “clinicians” about the utility and medical benefits of certain stem-cell therapies, sacrificing their time to debunk medical pseudoscience.

Using Curation and Science 2.0 to build Trusted, Expert Networks of Scientists and Clinicians

Establishing networks of trusted colleagues has been a cornerstone of the scientific discourse for centuries. For example, in the mid-1640s, the Royal Society began as:

“a meeting of natural philosophers to discuss promoting knowledge of the

natural world through observation and experiment”, i.e. science.

The Society met weekly to witness experiments and discuss what we

would now call scientific topics. The first Curator of Experiments

was Robert Hooke.”

– from The History of the Royal Society

The Royal Society of London for Improving Natural Knowledge.

(photo credit: Royal Society)

(Although one wonders why they met “in-cognito”)

Indeed as discussed in “Science 2.0/Brainstorming” by the originators of OpenWetWare, an open-source science-notebook software designed to foster open-innovation, the new search and aggregation tools are making it easier to find, contribute, and share information to interested individuals. This paradigm is the basis for the shift from Science 1.0 to Science 2.0. Science 2.0 is attempting to remedy current drawbacks which are hindering rapid and open scientific collaboration and discourse including:

Slow time frame of current publishing methods: reviews can take years to fashion leading to outdated material
Level of information dissemination is currently one dimensional: peer-review, highly polished work, conferences
Current publishing does not encourage open feedback and review
Published articles edited for print do not take advantage of new web-based features including tagging, search-engine features, interactive multimedia, no hyperlinks
Published data and methodology incomplete
Published data not available in formats which can be readably accessible across platforms: gene lists are now mandated to be supplied as files however other data does not have to be supplied in file format

(put in here a brief blurb of summary of problems and why curation could help)

Curation in the Sciences: View from Scientific Content Curators Larry H. Bernstein, MD, FCAP, Dr. Justin D. Pearlman, MD, PhD, FACC and Dr. Aviva Lev-Ari, PhD, RN

Curation is an active filtering of the web’s and peer reviewed literature found by such means – immense amount of relevant and irrelevant content. As a result content may be disruptive. However, in doing good curation, one does more than simply assign value by presentation of creative work in any category. Great curators comment and share experience across content, authors and themes. Great curators may see patterns others don’t, or may challenge or debate complex and apparently conflicting points of view. Answers to specifically focused questions comes from the hard work of many in laboratory settings creatively establishing answers to definitive questions, each a part of the larger knowledge-base of reference. There are those rare “Einstein’s” who imagine a whole universe, unlike the three blind men of the Sufi tale. One held the tail, the other the trunk, the other the ear, and they all said this is an elephant!
In my reading, I learn that the optimal ratio of curation to creation may be as high as 90% curation to 10% creation. Creating content is expensive. Curation, by comparison, is much less expensive.

– Larry H. Bernstein, MD, FCAP

Curation is Uniquely Distinguished by the Historical Exploratory Ties that Bind –Larry H. Bernstein, MD, FCAP

The explosion of information by numerous media, hardcopy and electronic, written and video, has created difficulties tracking topics and tying together relevant but separated discoveries, ideas, and potential applications. Some methods to help assimilate diverse sources of knowledge include a content expert preparing a textbook summary, a panel of experts leading a discussion or think tank, and conventions moderating presentations by researchers. Each of those methods has value and an audience, but they also have limitations, particularly with respect to timeliness and pushing the edge. In the electronic data age, there is a need for further innovation, to make synthesis, stimulating associations, synergy and contrasts available to audiences in a more timely and less formal manner. Hence the birth of curation. Key components of curation include expert identification of data, ideas and innovations of interest, expert interpretation of the original research results, integration with context, digesting, highlighting, correlating and presenting in novel light.

– Justin D Pearlman, MD, PhD, FACC from The Voice of Content Consultant on The Methodology of Curation in Cardiovascular Original Research: Cases in Methodology Design for Content Co-Curation The Art of Scientific & Medical Curation

In Power of Analogy: Curation in Music, Music Critique as a Curation and Curation of Medical Research Findings – A Comparison, Drs. Larry Bernstein and Aviva Lev-Ari likens the medical and scientific curation process to curation of musical works into a thematic program:

Work of Original Music Curation and Performance:

Music Review and Critique as a Curation

Work of Original Expression what is the methodology of Curation in the context of Medical Research Findings Exposition of Synthesis and Interpretation of the significance of the results to Clinical Care

… leading to new, curated, and collaborative works by networks of experts to generate (in this case) ebooks on most significant trends and interpretations of scientific knowledge as relates to medical practice.

In Summary: How Scientific Content Curation Can Help

Given the aforementioned problems of:

I. the complex and rapid deluge of scientific information

II. the need for a collaborative, open environment to produce transformative innovation

III. need for alternative ways to disseminate scientific findings

CURATION MAY OFFER SOLUTIONS

I. Curation exists beyond the review: curation decreases time for assessment of current trends adding multiple insights, analyses WITH an underlying METHODOLOGY (discussed below) while NOT acting as mere reiteration, regurgitation

II. Curation providing insights from WHOLE scientific community on multiple WEB 2.0 platforms

III. Curation makes use of new computational and Web-based tools to provide interoperability of data, reporting of findings (shown in Examples below)

Therefore a discussion is given on methodologies, definitions of best practices, and tools developed to assist the content curation community in this endeavor.

Methodology in Scientific Content Curation as Envisioned by Aviva lev-Ari, PhD, RN

At Leaders in Pharmaceutical Business Intelligence, site owner and chief editor Aviva lev-Ari, PhD, RN has been developing a strategy “for the facilitation of Global access to Biomedical knowledge rather than the access to sheer search results on Scientific subject matters in the Life Sciences and Medicine”. According to Aviva, “for the methodology to attain this complex goal it is to be dealing with popularization of ORIGINAL Scientific Research via Content Curation of Scientific Research Results by Experts, Authors, Writers using the critical thinking process of expert interpretation of the original research results.” The following post:

Cardiovascular Original Research: Cases in Methodology Design for Content Curation and Co-Curation

http://pharmaceuticalintelligence.com/2013/07/29/cardiovascular-original-research-cases-in-methodology-design-for-content-curation-and-co-curation/

demonstrate two examples how content co-curation attempts to achieve this aim and develop networks of scientist and clinician curators to aid in the active discussion of scientific and medical findings, and use scientific content curation as a means for critique offering a “new architecture for knowledge”. Indeed, popular search engines such as Google, Yahoo, or even scientific search engines such as NCBI’s PubMed and the OVID search engine rely on keywords and Boolean algorithms …

which has created a need for more context-driven scientific search and discourse.

In Science and Curation: the New Practice of Web 2.0, Célya Gruson-Daniel (@HackYourPhd) states:

To address this need, human intermediaries, empowered by the participatory wave of web 2.0, naturally started narrowing down the information and providing an angle of analysis and some context. They are bloggers, regular Internet users or community managers – a new type of profession dedicated to the web 2.0. A new use of the web has emerged, through which the information, once produced, is collectively spread and filtered by Internet users who create hierarchies of information.

.. where Célya considers curation an essential practice to manage open science and this new style of research.

As mentioned above in her article, Dr. Lev-Ari represents two examples of how content curation expanded thought, discussion, and eventually new ideas.

Curator edifies content through analytic process = NEW form of writing and organizations leading to new interconnections of ideas = NEW INSIGHTS

i) Evidence: curation methodology leading to new insights for biomarkers

Same as #1 but multiple players (experts) each bringing unique insights, perspectives, skills yielding new research = NEW LINE of CRITICAL THINKING

ii) Evidence: co-curation methodology among cardiovascular experts leading to cardiovascular series ebooks

The Life Cycle of Science 2.0. Due to Web 2.0, new paradigms of scientific collaboration are rapidly emerging. Originally, scientific discovery were performed by individual laboratories or “scientific silos” where the main method of communication was peer-reviewed publication, meeting presentation, and ultimately news outlets and multimedia. In this digital era, data was organized for literature search and biocurated databases. In an era of social media, Web 2.0, a group of scientifically and medically trained “curators” organize the piles of data of digitally generated data and fit data into an organizational structure which can be shared, communicated, and analyzed in a holistic approach, launching new ideas due to changes in organization structure of data and data analytics.

The result, in this case, is a collaborative written work above the scope of the review. Currently review articles are written by experts in the field and summarize the state of a research are. However, using collaborative, trusted networks of experts, the result is a real-time synopsis and analysis of the field with the goal in mind to

INCREASE THE SCIENTIFIC CURRENCY.

For detailed description of methodology please see Cardiovascular Original Research: Cases in Methodology Design for Content Co-Curation The Art of Scientific & Medical Curation

In her paper, Curating e-Science Data, Maureen Pennock, from The British Library, emphasized the importance of using a diligent, validated, and reproducible, and cost-effective methodology for curation by e-science communities over the ‘Grid’:

“The digital data deluge will have profound repercussions for the infrastructure of research and beyond. Data from a wide variety of new and existing sources will need to be annotated with metadata, then archived and curated so that both the data and the programmes used to transform the data can be reproduced for use in the future. The data represent a new foundation for new research, science, knowledge and discovery”

— JISC Senior Management Briefing Paper, The Data Deluge (2004)

As she states proper data and content curation is important for:

Post-analysis
Data and research result reuse for new research
Validation
Preservation of data in newer formats to prolong life-cycle of research results

However she laments the lack of

Funding for such efforts
Training
Organizational support
Monitoring
Established procedures

Tatiana Aders wrote a nice article based on an interview with Microsoft’s Robert Scoble, where he emphasized the need for curation in a world where “Twitter is the replacement of the Associated Press Wire Machine” and new technologic platforms are knocking out old platforms at a rapid pace. In addition he notes that curation is also a social art form where primary concerns are to understand an audience and a niche.

Indeed, part of the reason the need for curation is unmet, as writes Mark Carrigan, is the lack of appreciation by academics of the utility of tools such as Pinterest, Storify, and Pearl Trees to effectively communicate and build collaborative networks.

And teacher Nancy White, in her article Understanding Content Curation on her blog Innovations in Education, shows examples of how curation in an educational tool for students and teachers by demonstrating students need to CONTEXTUALIZE what the collect to add enhanced value, using higher mental processes such as:

Knowledge
Comprehension
Application
Analysis
Synthesis
Evaluation

A GREAT table about the differences between Collecting and Curating by Nancy White at http://d20innovation.d20blogs.org/2012/07/07/understanding-content-curation/

University of Massachusetts Medical School has aggregated some useful curation tools at http://esciencelibrary.umassmed.edu/data_curation

Although many tools are related to biocuration and building databases but the common idea is curating data with indexing, analyses, and contextual value to provide for an audience to generate NETWORKS OF NEW IDEAS.

See here for a curation of how networks fosters knowledge, by Erika Harrison on ScoopIt

(http://www.scoop.it/t/mobilizing-knowledge-through-complex-networks)

“Nowadays, any organization should employ network scientists/analysts who are able to map and analyze complex systems that are of importance to the organization (e.g. the organization itself, its activities, a country’s economic activities, transportation networks, research networks).”

– Andrea Carafa insight from World Economic Forum New Champions 2012 “Power of Networks”

Creating Content Curation Communities: Breaking Down the Silos!

An article by Dr. Dana Rotman “Facilitating Scientific Collaborations Through Content Curation Communities” highlights how scientific information resources, traditionally created and maintained by paid professionals, are being crowdsourced to professionals and nonprofessionals in which she termed “content curation communities”, consisting of professionals and nonprofessional volunteers who create, curate, and maintain the various scientific database tools we use such as Encyclopedia of Life, ChemSpider (for Slideshare see here), biowikipedia etc. Although very useful and openly available, these projects create their own challenges such as

information integration (various types of data and formats)
social integration (marginalized by scientific communities, no funding, no recognition)

The authors set forth some ways to overcome these challenges of the content curation community including:

standardization in practices
visualization to document contributions
emphasizing role of information professionals in content curation communities
maintaining quality control to increase respectability
recognizing participation to professional communities
proposing funding/national meeting – Data Intensive Collaboration in Science and Engineering Workshop

A few great presentations and papers from the 2012 DICOSE meeting are found below

Judith M. Brown, Robert Biddle, Stevenson Gossage, Jeff Wilson & Steven Greenspan. Collaboratively Analyzing Large Data Sets using Multitouch Surfaces. (PDF) NotesForBrown

Bill Howe, Cecilia Aragon, David Beck, Jeffrey P. Gardner, Ed Lazowska, Tanya McEwen. Supporting Data-Intensive Collaboration via Campus eScience Centers. (PDF) NotesForHowe

Kerk F. Kee & Larry D. Browning. Challenges of Scientist-Developers and Adopters of Existing Cyberinfrastructure Tools for Data-Intensive Collaboration, Computational Simulation, and Interdisciplinary Projects in Early e-Science in the U.S.. (PDF) NotesForKee

Ben Li. The mirages of big data. (PDF) NotesForLi ReflectionsByBen

Betsy Rolland & Charlotte P. Lee. Post-Doctoral Researchers’ Use of Preexisting Data in Cancer Epidemiology Research. (PDF) NoteForRolland

Dana Rotman, Jennifer Preece, Derek Hansen & Kezia Procita. Facilitating scientific collaboration through content curation communities. (PDF) NotesForRotman

Nicholas M. Weber & Karen S. Baker. System Slack in Cyberinfrastructure Development: Mind the Gaps. (PDF) NotesForWeber

Indeed, the movement of Science 2.0 from Science 1.0 had originated because these “silos” had frustrated many scientists, resulting in changes in the area of publishing (Open Access) but also communication of protocols (online protocol sites and notebooks like OpenWetWare and BioProtocols Online) and data and material registries (CGAP and tumor banks). Some examples are given below.

Open Science Case Studies in Curation

1. Open Science Project from Digital Curation Center

This project looked at what motivates researchers to work in an open manner with regard to their data, results and protocols, and whether advantages are delivered by working in this way.

The case studies consider the benefits and barriers to using ‘open science’ methods, and were carried out between November 2009 and April 2010 and published in the report Open to All? Case studies of openness in research. The Appendices to the main report (pdf) include a literature review, a framework for characterizing openness, a list of examples, and the interview schedule and topics. Some of the case study participants kindly agreed to us publishing the transcripts. This zip archive contains transcripts of interviews with researchers in astronomy, bioinformatics, chemistry, and language technology.

see: Pennock, M. (2006). “Curating e-Science Data”. DCC Briefing Papers: Introduction to Curation. Edinburgh: Digital Curation Centre. Handle: 1842/3330. Available online: http://www.dcc.ac.uk/resources/briefing-papers/introduction-curation– See more at: http://www.dcc.ac.uk/resources/briefing-papers/introduction-curation/curating-e-science-data#sthash.RdkPNi9F.dpuf

2. cBIO -cBio’s biological data curation group developed and operates using a methodology called CIMS, the Curation Information Management System. CIMS is a comprehensive curation and quality control process that efficiently extracts information from publications.

3. NIH Topic Maps – This website provides a database and web-based interface for searching and discovering the types of research awarded by the NIH. The database uses automated, computer generated categories from a statistical analysis known as topic modeling.

4. SciKnowMine (USC)- We propose to create a framework to support biocuration called SciKnowMine (after ‘Scientific Knowledge Mine’), cyberinfrastructure that supports biocuration through the automated mining of text, images, and other amenable media at the scale of the entire literature.

OpenWetWare– OpenWetWare is an effort to promote the sharing of information, know-how, and wisdom among researchers and groups who are working in biology & biological engineering. Learn more about us. If you would like edit access, would be interested in helping out, or want your lab website hosted on OpenWetWare, pleasejoin us. OpenWetWare is managed by the BioBricks Foundation. They also have a wiki about Science 2.0.

6. LabTrove: a lightweight, web based, laboratory “blog” as a route towards a marked up record of work in a bioscience research laboratory. Authors in PLOS One article, from University of Southampton, report the development of an open, scientific lab notebook using a blogging strategy to share information.

7. OpenScience Project– The OpenScience project is dedicated to writing and releasing free and Open Source scientific software. We are a group of scientists, mathematicians and engineers who want to encourage a collaborative environment in which science can be pursued by anyone who is inspired to discover something new about the natural world.

8. Open Science Grid is a multi-disciplinary partnership to federate local, regional, community and national cyberinfrastructures to meet the needs of research and academic communities at all scales.

9. Some ongoing biomedical knowledge (curation) projects at ISI

IICurate
This project is concerned with developing a curation and documentation system for information integration in collaboration with the II Group at ISI as part of the BIRN.

BioScholar
It’s primary purpose is to provide software for experimental biomedical scientists that would permit a single scientific worker (at the level of a graduate student or postdoctoral worker) to design, construct and manage a shared knowledge repository for a research group derived on a local store of PDF files. This project is funded by NIGMS from 2008-2012 ( RO1-GM083871).

10. Tools useful for scientific content curation

Research Analytic and Curation Tools from University of Queensland

Thomson Reuters information curation services for pharma industry

Microblogs as a way to communicate information about HPV infection among clinicians and patients; use of Chinese microblog SinaWeibo as a communication tool

VIVO for scientific communities– In order to connect this information about research activities across institutions and make it available to others, taking into account smaller players in the research landscape and addressing their need for specific information (for example, by proving non-conventional research objects), the open source software VIVO that provides research information as linked open data (LOD) is used in many countries. So-called VIVO harvesters collect research information that is freely available on the web, and convert the data collected in conformity with LOD standards. The VIVO ontology builds on prevalent LOD namespaces and, depending on the needs of the specialist community concerned, can be expanded.

11. Examples of scientific curation in different areas of Science/Pharma/Biotech/Education

From Science 2.0 to Pharma 3.0 Q&A with Hervé Basset

http://digimind.com/blog/experts/pharma-3-0/

Hervé Basset, specialist librarian in the pharmaceutical industry and owner of the blog “Science Intelligence“, to talk about the inspiration behind his recent book entitled “From Science 2.0 to Pharma 3.0″, published by Chandos Publishing and available on Amazon and how health care companies need a social media strategy to communicate and convince the health-care consumer, not just the practicioner.

Thomson Reuters and NuMedii Launch Ground-Breaking Initiative to Identify Drugs for Repurposing. Companies leverage content, Big Data analytics and expertise to improve success of drug discovery

Content Curation as a Context for Teaching and Learning in Science

#OZeLIVE Feb2014

http://www.youtube.com/watch?v=Ty-ugUA4az0

Creative Commons license

DigCCur: A graduate level program initiated by University of North Carolina to instruct the future digital curators in science and other subjects

Syracuse University offering a program in eScience and digital curation

Curation Tips from TED talks and tech experts

Steven Rosenbaum from Curation Nation

http://www.youtube.com/watch?v=HpncJd1v1k4

Pawan Deshpande form Curata on how content curation communities evolve and what makes a good content curation:

http://www.youtube.com/watch?v=QENhIU9YZyA

How the Internet of Things is Promoting the Curation Effort

Update by Stephen J. Williams, PhD 3/01/19

Up till now, curation efforts like wikis (Wikipedia, Wikimedicine, Wormbase, GenBank, etc.) have been supported by a largely voluntary army of citizens, scientists, and data enthusiasts. I am sure all have seen the requests for donations to help keep Wikipedia and its other related projects up and running. One of the obscure sister projects of Wikipedia, Wikidata, wants to curate and represent all information in such a way in which both machines, computers, and humans can converse in. About an army of 4 million have Wiki entries and maintain these databases.

Enter the Age of the Personal Digital Assistants (Hellooo Alexa!)

In a March 2019 WIRED article “Encyclopedia Automata: Where Alexa Gets Its Information” senior WIRED writer Tom Simonite reports on the need for new types of data structure as well as how curated databases are so important for the new fields of AI as well as enabling personal digital assistants like Alexa or Google Assistant decipher meaning of the user.

As Mr. Simonite noted, many of our libraries of knowledge are encoded in an “ancient technology largely opaque to machines-prose.” Search engines like Google do not have a problem with a question asked in prose as they just have to find relevant links to pages. Yet this is a problem for Google Assistant, for instance, as machines can’t quickly extract meaning from the internet’s mess of “predicates, complements, sentences, and paragraphs. It requires a guide.”

Enter Wikidata. According to founder Denny Vrandecic,

Language depends on knowing a lot of common sense, which computers don’t have access to

A wikidata entry (of which there are about 60 million) codes every concept and item with a numeric code, the QID code number. These codes are integrated with tags (like tags you use on Twitter as handles or tags in WordPress used for Search Engine Optimization) so computers can identify patterns of recognition between these codes.

Now human entry into these databases are critical as we add new facts and in particular meaning to each of these items. Else, machines have problems deciphering our meaning like Apple’s Siri, where they had complained of dumb algorithms to interpret requests.

The knowledge of future machines could be shaped by you and me, not just tech companies and PhDs.

But this effort needs money

Wikimedia’s executive director, Katherine Maher, had prodded and cajoled these megacorporations for tapping the free resources of Wiki’s. In response, Amazon and Facebook had donated millions for the Wikimedia projects. Google recently gave 3.1 million USD$ in donations.

Future postings on the relevance and application of scientific curation will include:

Using Scientific Content Curation as a Method for Validation and Biocuration

Using Scientific Content Curation as a Method for Open Innovation

Other posts on this site related to Content Curation and Methodology include:

The growing importance of content curation

Data Curation is for Big Data what Data Integration is for Small Data

6 Steps to More Effective Content Curation

Stem Cells and Cardiac Repair: Content Curation & Scientific Reporting

Cancer Research: Curations and Reporting

Cardiovascular Diseases and Pharmacological Therapy: Curations

Cardiovascular Original Research: Cases in Methodology Design for Content Co-Curation The Art of Scientific & Medical Curation

Exploring the Impact of Content Curation on Business Goals in 2013

Power of Analogy: Curation in Music, Music Critique as a Curation and Curation of Medical Research Findings – A Comparison

conceived: NEW Definition for Co-Curation in Medical Research

The Young Surgeon and The Retired Pathologist: On Science, Medicine and HealthCare Policy – The Best Writers Among the WRITERS

Reconstructed Science Communication for Open Access Online Scientific Curation

Read Full Post »

Good and Bad News Reported for Ovarian Cancer Therapy

Posted in Biological Networks, Gene Regulation and Evolution, CANCER BIOLOGY & Innovations in Cancer Therapy, Cancer Prevention: Research & Programs, Cell Biology, Signaling & Cell Circuits, Computational Biology/Systems and Bioinformatics, Disease Biology, Small Molecules in Development of Therapeutic Drugs, FDA Regulatory Affairs, FDA, CE Mark & Global Regulatory Affairs: process management and strategic planning - GCP, GLP, ISO 14155, Health Economics and Outcomes Research, Personalized and Precision Medicine & Genomic Research, Pharmaceutical Drug Discovery, Pharmaceutical Industry Competitive Intelligence, Pharmaceutical R&D Investment, Population Health Management, Genetics & Pharmaceutical, Translational Science, Uncategorized, tagged AstraZeneca, BRCA mutation, BRCA1, BRCA2, breast cancer, Cancer - General, Chemotherapy, Clinical trial, Conditions and Diseases, DNA repair, National Institutes of Health, olaparib, ovarian cancer, PARP-1 inhibitor, Pfizer, Prostate cancer, research on July 1, 2014| Leave a Comment »

Good and Bad News Reported for Ovarian Cancer Therapy

Reporter, Curator: Stephen J. Williams, Ph.D.

In a recent Fierce Biotech report

“FDA review red-flags AstraZeneca’s case for ovarian cancer drug olaparib”,

John Carroll reports on a disappointing ruling by the FDA on AstraZeneca’s PARP1 inhibitor olaparib for maintenance therapy in women with cisplatin refractory ovarian cancer with BRCA mutation. Early clinical investigations had pointed to efficacy of PARP inhibitors in ovarian tumors carrying the BRCA mutation. The scientific rationale for using PARP1 inhibitors in BRCA1/2 deficiency was quite clear:

DNA damage can result in

1. double strand breaks (DSB)

DSB can be repaired by efficient homologous recombination (HR) or less efficient non-homologous end joining (NHEJ)

b. BRCA1 involved in RAD51 dependent HR at DSB sites

In BRCA1 deficiency DSB repaired by less efficient NHEJ

2. single strand breaks, damage (SSB)

PARP1 is activated by DNA damage and poly-ADP ribosylates histones and other proteins marking DNA for SSB repair
SSB repair usually base excision (BER) or sometimes nucleotide excision repair (NER)

B. if PARP inhibited then SSB gets converted to DSB

C. in BRCA1/2 deficient background repair is forced to less efficient NHEJ thereby perpetuating some DNA damage pon exposure to DNA damaging agent

A good review explaining the pharmacology behind the rationale of PARP inhibitors in BRCA deficient breast and ovarian cancer is given by Drs. Christina Annunziata and Susan E. Bates in PARP inhibitors in BRCA1/BRCA2 germline mutation carriers with ovarian and breast cancer

(http://f1000.com/prime/reports/b/2/10/) and below a nice figure from their paper:

(from Christina M Annunziata and Susan E Bates. PARP inhibitors in BRCA1/BRCA2 germline mutation carriers with ovarian and breast cancer. F1000 Biol Reports, 2010; 2:10.) Creative Commons

Dr. Sudipta Saha’s post BRCA1 a tumour suppressor in breast and ovarian cancer – functions in transcription, ubiquitination and DNA repair discusses how BRCA1 affects the double strand DNA repair process, augments histone modification, as well as affecting expression of DNA repair genes.

Dana Farber’s Dr. Ralph Scully, Ph.D., in Exploiting DNA Repair Targets in Breast Cancer (http://www.dfhcc.harvard.edu/news/news/article/5402/), explains his research investigating why multiple DNA repair pathways may have to be targeted with PARP therapy concurrent with BRCA1 deficiency.

However FDA investigators voiced their skepticism of AstraZeneca’s clinical results, namely

Small number of patients enrolled
BRCA1/2 cohort were identified retrospectively
results skewed by false benefit from “underperforming” control arm
possible inadvertent selection bias
hazard ratio suggesting improvement in progression free survival but higher risk/benefit

The FDA investigators released their report two days before an expert panel would be releasing their own report (reported in the link below from FierceBiotech)

UPDATED: FDA experts spurn AstraZeneca’s pitch for ovarian cancer drug olaparib

in which the expert panel reiterated the findings of the FDA investigators. The expert panel’s job was to find if there was any clinical benefit for continuing consideration of olaparib, basically stating

“This trial has problems,” noted FDA cancer chief Richard Pazdur during the panel discussion. If investigators had “pristine evidence of a 7-month advantage in PFS, we wouldn’t be here.”

The expert panel was concerned for the above reasons as well as the reported handful of lethal cases of myelodysplastic syndrome and acute myeloid leukemia in the study, although the panel noted these patients had advanced disease before entering the trial, raising the possibility that prior drugs may have triggered their deaths.

This was certainly a disappointment as ….

it was at last year’s ASCO (2013) that investigators at Perelman School of Medicine at the University of Pennsylvania and Sheba Medical Center in Tel Hashomer, Israel presented data showing that in 193 cisplatin-refractory ovarian cancer patients carrying a BRCA1/2 mutation, 31% had a partial or complete tumor regression. In addition the study also showed good response in pancreatic and prostate cancer with tolerable side effects.

See here for study details: http://www.uphs.upenn.edu/news/News_Releases/2013/05/domchek/

As John Carrol from FierceBiotech notes, the decision may spark renewed interest by Pfizer of a bid for AstraZeneca as the potential FDA rejection would certainly dampen AstraZeneca’s future growth and profit plans. Last month AstraZeneca’s CEO made the case to shareholders to reject the Pfizer offer by pointing to AstraZeneca’s potential beefed-up pipeline. AstraZeneca had projected olaparib as a potential $2 billion-a-year seller, although some industry analysts see sales at less than half that amount.

A company spokeswoman said the monotherapy use of olaparib for ovarian cancer assessed by the U.S. expert panel this week was only one element of a broad development program.

Please see a table of current oncology clinical trials with PARP1 inhibitors

at end of this post

However, on the same day, FierceBiotechreports some great news (at least in Europe) on the ovarian cancer front:

EU backs Roche’s Avastin for hard-to-treat ovarian cancer

As Arlene Weintraub of FierceBiotech reports:

EU Committee for Medicinal Products for Human Use (CHMP) handed down a positive ruling on Avastin, recommending that the European Commission approve the drug for use in women with ovarian cancer that’s resistant to platinum-based chemotherapy. It’s the first biologic to receive a positive opinion from the CHMP for this hard-to-treat form of the disease.

Please see here for official press release: CHMP recommends EU approval of Roche’s Avastin for platinum-resistant recurrent ovarian cancer

EU had been getting pressure from British doctors to approve Avastin based on clinical trial results although it may be important to note that the EU zone seems to have an ability to recruit more numbers for clinical trials than in US. For instance an EU women’s breast cancer prevention trial had heavy recruitment in what would be considered a short time frame compared to recruitment times for the US.

Below is a table on PARP1 inhibitors in current clinical trials (obtained from NewMedicine’s Oncology KnowledgeBase™). nm|OK is a relational knowledgeBASE covering all major aspects of product development in oncolology. The database comprises 6 modules each dedicated in a specific sector within the oncology field.

PARP1 Inhibitors Currently in Clinical Trials for Ovarian Cancer

Developer and Drug Name	Development Status & Location – Indications
AbbVie Current as of: March 27, 2014 PARP inhibitor: ABT-767	Phase I (begin 5/11, ongoing 2/14) Europe (Netherlands) – solid tumors with BRCA1 or BRCA2 mutations, locally advanced or metastatic • ovarian cancer, advanced or metastatic • fallopian tube cancer, advanced or metastatic • peritoneal cancer, advanced or metastatic
AstraZeneca Affiliate(s): · Myriad GeneticsCurrent as of: June 26, 2014Generic Name: Olaparib Brand Name: Lynparza Other Designation: AZD2281, KU59436, KU-0059436, NSC 747856	Phase I (begin 7/05, closed 9/08) Europe (Netherlands, UK, Poland); phase II (begin 6/07, closed 2/08, completed 5/09) USA, Australia, Europe (Germany, Spain, Sweden, UK), phase II (begin 7/08, closed 2/09) USA, Australia, Europe (Belgium, Germany, Poland, Spain, UK), Israel, phase II (begin 8/08, closed 12/09, completed 3/13) USA, Australia, Canada, Europe (Belgium, France, Germany, Poland, Romania, Spain, Ukraine, UK), Israel, Russia; phase II (begin 2/10, closed 7/10) USA, Australia, Canada, Europe (Belgium, Czech Republic, Germany, Italy, Netherlands, Spain, UK), Japan, Panama, Peru (combination); MAA (accepted 9/13) EU, NDA (filed 2/14) USA – ovarian cancer, advanced or metastatic, BRCA positive • ovarian cancer, recurrent, platinum sensitive • ovarian cancer, advanced, refractory, BRCA1 or BRCA2-associatedPhase I (begin 5/08, ongoing 5/12) USA; phase II (begin 7/08, closed 10/09) Canada – breast cancer, locally advanced, BRCA1/BRCA2-associated or hereditary metastatic or inoperable • ovarian cancer, locally advanced, BRCA1/BRCA2-associated or hereditary metastatic or inoperable • breast cancer, triple-negative, BRCA-positive • ovarian cancer, high-grade serous and/or undifferentiated, BRCA-positive Phase I (begin 10/10, ongoing 1/13) USA (combination) – ovarian cancer, inoperable or metastatic, refractory • breast cancer, inoperable or metastatic, refractory Phase III (begin 8/13) USA, Australia, Brazil, Canada, Europe (France, Italy, Netherlands, Poland, Russia, Spain, UK), Israel, South Korea, phase III (begin 9/13) USA, Australia, Brazil, Canada, Europe (France, Germany, Italy, Netherlands, Poland, Russia, Spain, UK), Israel – ovarian cancer, serous, high grade, BRCA mutated, platinum-sensitive, relapsed, third line, maintenance • ovarian cancer, serous or endometrioid, high grade, BRCA mutated, platinum responsive (PR or CR), maintenance, first line • primary peritoneal cancer, high grade, BRCA mutated, platinum responsive (PR or CR), maintenance • fallopian tube cancer, high grade, BRCA mutated, platinum responsive (PR or
BioMarin Pharmaceutical Current as of: June 14, 2014 PARP inhibitor: BMN-673, BMN673, LT-673	Phase I/II (begin 1/11, ongoing 3/14) USA – solid tumors, advanced, recurrent Phase I (begin 2/13, closed 4/13, completed 5/14) USA – healthy volunteers Phase I/II (begin 11/13) USA – solid tumors, relapsed or refractory, BRCA mutated, second line
BiPar Sciences Current as of: April 16, 2009 Parp inhibitor: BSI-401	Preclin (ongoing 4/09) – solid tumors
Clovis Oncology Affiliate(s): · University of Newcastle Upon Tyne · Cancer Research Campaign Technology · PfizerCurrent as of: June 21, 2014Generic Name: Rucaparib Brand Name: Rucapanc Other Designation: AG140699, AG014699, AG-14,699, AG-14669, AG14699, AG140361, AG-14361, AG-014699, CO-338, PF-01367338	Phase I (begin 03, completed 05) Europe (UK) (combination), phase I (begin 2/10, closed 11/13) Europe (France, UK) (combination) – solid tumors, advanced Phase II (begin 12/07, closed 10/13) Europe (UK) – breast cancer, advanced or metastatic, in patients carrying BRCA1 or BRCA2 mutations • ovarian cancer, advanced or metastatic, in patients carrying BRCA1 or BRCA2 mutations Phase I/II (begin 11/11, ongoing 6/14) USA, Europe (UK) – solid tumors, metastatic, with mutated BRCA • breast cancer, metastatic, HEr2 negative, with mutated BRCA
Sanofi Current as of: June 03, 2013 Generic Name: Iniparib Brand Name: Tivolza Other Designation: BSI-201, NSC 746045, SAR240550	Phase I/Ib (begin 3/06, closed 3/10) USA (combination), phase I (begin 7/10, closed 11/10) USA, phase I (begin 9/10, ongoing 2/11) Japan (combination); phase Ib (begin 1/07, ongoing 1/11) USA (combination) – solid tumors, advanced, refractory Phase II (begin 5/08, closed 1/09) USA – ovarian cancer, advanced, refractory, BRCA-1 or BRCA-2 associated • fallopian tube cancer, advanced, refractory, BRCA-1 or BRCA-2 associated • peritoneal cancer, advanced, refractory, BRCA-1 or BRCA-2 associated
Tesaro Affiliate(s): · MerckCurrent as of: May 18, 2014Generic Name: Niraparib Other Designation: MK-4827, MK4827	Phase I (begin 9/08, closed 2/11) USA, Europe (UK) – solid tumors, locally advanced or metastatic • ovarian cancer, locally advanced or metastatic, BRCA mutant • chronic lymphocytic leukemia (CLL), relapsed or refractory • prolymphocytic leukemia, T cell, relapsed or refractory Phase Ib (begin 11/10, closed 3/11, terminated 10/12) USA (combination) – solid tumors, locally advanced or metastatic • ovarian cancer, serous, high grade, platinum resistant or refractoryPhase III (begin 5/13, ongoing 5/14) USA – ovarian cancer, platinum-sensitive, high grade serous or BRCA mutant, chemotherapy responsive • fallopian tube cancer • primary peritoneal cancer
Teva Pharmaceutical Industries Current as of: May 04, 2013 Designation: CEP-9722	Phase I (begin 5/11, closed 11/12, terminated 10/13) USA, phase I (begin 6/09, closed 7/12, completed 1/12) Europe (France and UK) (combination) – solid tumors, advanced, third line Phase I (begin 5/11, completed 1/13) Europe (France) (combination) – solid tumors, advanced • mantle cell lymphoma (MCL), advanced

Summary of Combination Ovarian Cancer Trials with Avastin (current and closed)

Indication in Development	ovarian cancer, advanced, recurrent, persistent • ovarian cancer, progressive, platinum resistant, second line • fallopian tube cancer, progressive, platinum resistant, second line • primary peritoneal cancer, progressive, platinum resistant, second line
Latest Status	Phase II (begin 4/02, closed 8/04) USA, phase II (begin 11/04, closed 10/05) USA; phase III (begin 10/09) Europe (Belgium, Bosnia and Herzegovina, Denmark, Finland, France, Germany, Greece, Italy, Netherlands, Norway, Portugal, Spain, Sweden), Turkey
Clinical History	Refer to the Combination Trial Module for trials of Avastin in combination with various chemotherapeutic regimens.According to results from the AURELIA clinical trial (protocol ID: MO22224; 2009-011400-33; NCT00976911), the median PFS in women with progressive platinum resistant ovarian, fallopian tube or primary peritoneal cancer treated with Avastin in combination with chemotherapy, was 6.7 months compared to 3.4 months in those treated with chemotherapy alone for an HR of 0.48 (range =0.38–0.60).. In addition, the objective response rate was 30.9% in women treated with Avastin compared to 12.6% in those on chemotherapy (p=0.001). Certain AE (Grade 2 to 5) that occurred more often in the Avastin arm compared to the chemotherapy alone arm were high blood pressure (20% versus 7%) and an excess of protein in the urine (11% versus 1%). Gastrointestinal perforations and fistulas occurred in 2% of women in the Avastin arm compared to no events in the chemotherapy arm (Pujade-Lauraine E, etal, ASCO12, Abs. LBA5002).A multicenter (n=124), randomized, open label, 2-arm, phase III clinical trial (protocol ID: MO22224; 2009-011400-33; NCT00976911; http://clinicaltrials.gov/ct2/results?term=NCT00976911 ), dubbed AURELIA, was initiated in October 2009, in Europe (Belgium, Bosnia and Herzegovina, Denmark, Finland, France, Germany, Greece, Italy, Netherlands, Norway, Portugal, Spain, and Sweden), and Turkey, to evaluate the efficacy and safety of Avastin added to chemotherapy versus chemotherapy alone in patients with epithelial ovarian, fallopian tube or primary peritoneal cancer with disease progression within 6 months of platinum therapy in the first line setting. The trials primary outcome measure is PFS. Secondary outcome measures include objective response rate, biological PFS interval, OS, QoL, and safety and tolerability. According to the protocol, all patients are treated with standard chemotherapy with IV paclitaxel (80 mg/m²) on days 1, 8, 15 and 22 of each 4-week cycle; or IV topotecan at a dose of 4 mg/m² on days 1, 8 and 15 of each 4-week cycle, or 1.25 mg/kg on days 1-5 of each 3-week cycle; or IV liposomal doxorubicin (40 mg/m²) every 4 weeks. Patients (n=179) randomized to arm 2 of the trial are treated with IV Avastin at a dose of 10 mg/kg twice weekly or 15 mg/kg thrice weekly concomitantly with the chemotherapy choice. Treatment continues until disease progression. Subsequently, patients are treated with the standard of care. Patients in arm 1 (n=182), on chemotherapy only may opt to be treated with IV Avastin (15 mg/kg) three times weekly. The trial was set up in cooperation with the Group d’Investigateurs Nationaux pour l’Etude des Cancers Ovariens (GINECO) and was conducted by the international network of the Gynecologic Cancer Intergroup (GCIG) and the pan-European Network of Gynaecological Oncological Trial Groups (ENGOT), under PI Eric Pujade-Lauraine, MD, Hopitaux Universitaires, Paris Centre, Hôpital Hôtel-Dieu (Paris, France). The trial enrolled 361 patients and was closed as of May 2012..Results were presented from a phase II clinical trial (protocol ID: CDR0000068839; GOG-0170D; NCT00022659) of bevacizumab in patients with persistent or recurrent epithelial ovarian cancer or primary peritoneal cancer that was performed by the Gynecologic Oncology Group to determine the ORR, PFS, and toxicity for this treatment. Patients must have been administered 1-2 prior cytotoxic regimens. Treatment consisted of bevacizumab (15 mg/kg) IV every 3 weeks until disease progression or prohibitive toxicity. Between April 2002 and August 2004, 64 patients were enrolled, of which 2 were excluded for wrong primary and borderline histology and 62 were evaluable (1 previous regimen=23, 2 previous regimens=39). The median disease free interval from completion of primary cytotoxic chemotherapy to first recurrence was 6.5 months. Early results demonstrated that some patients had confirmed objective responses and PFS in some was at least 6 months. Observed Grade 3 or 4 toxicities included allergy (Grade 3=1), cardiovascular (Grade 3=4; Grade 4=1), gastrointestinal (Grade 3=3), hepatic (Grade 3=1), pain (Grade 3=2), and pulmonary (Grade 4=1). As of 11/04, 36 patients were removed from the trial, including 29 for disease progression and 1 for toxicity in 33 cases reported. Preliminary evidence exists for objective responses to bevacizumab (Burger R, et al, ASCO05, Abs. 5009).An open label, single arm, 2-stage, phase II clinical trial (protocol ID: AVF2949g, NCT00097019) of bevacizumab in patients with platinum resistant, advanced (Stage III or IV), ovarian cancer or primary peritoneal cancer for whom subsequent doxorubicin or topotecan therapy also has failed was initiated in November 2004 at multiple locations in the USA to determine the safety and efficacy for this treatment.A multicenter phase II clinical trial was initiated in April 2002 to determine the 6-month PFS of patients with persistent or recurrent ovarian epithelial or primary peritoneal cancer treated with bevacizumab (protocol ID: GOG-0170D, CDR0000068839, NCT00022659). IV bevacizumab is administered over 30-90 minutes on day 1. Treatment is repeated every 21 days in the absence of disease progression or unacceptable toxicity. Patients are followed every 3 months for 2 years, every 6 months for 3 years, and then annually thereafter. A total of 22-60 patients will be accrued within 12-30 months. Robert A. Burger, MD, of Chao Family Comprehensive Cancer Center is Trial Chair.This trial was closed in August 2004.

Sources

http://www.fiercebiotech.com/story/fda-review-red-flags-astrazenecas-case-ovarian-cancer-drug-olaparib/2014-06-23

http://www.fiercebiotech.com/story/fda-experts-spurn-astrazenecas-pitch-ovarian-cancer-drug-olaparib/2014-06-25

http://www.fiercepharma.com/story/eu-backs-roches-avastin-hard-treat-ovarian-cancer/2014-06-27

In a followup to this original posting A Report From the Institute of Medicine of the National Academies of Sciences, Engineering, and Medicine entitled

Evolving Approaches in Research and Care for Ovarian Cancers

was generated in a ViewPoint piece in JAMA which discussed their Congressional mandated report on the State of the Science in Ovarian Cancer Research, titled

Ovarian Cancers: Evolving Paradigms in Research and Care

highlights some of the research gaps felt by the committee in the current state of ovarian cancer research including:

consideration in research protocols of the multitude of histologic and morphologic subtypes of ovarian cancer, including the feeling of the committee that high grade serous OVCA originates from the distal end of the fallopian tube (espoused by Dr. Doubeau and Dr. Christopher Crum) versus originating from the ovarian surface epithelium
a call for expanded screening and prevention research with mutimodal screening including CA125 with secondary transvaginal screen
better patient education of the risk/benefit of genetic testing including BRCA1/2 as well as in consideration for PARP inhibitor therapy
treatments should be standardized and disseminated including more research in health outcomes and decision support for personalized therapy

This Perspective article can be found here: jvp160038

Some other posts relating to OVARIAN CANCER on this site include

Efficacy of Ovariectomy in Presence of BRCA1 vs BRCA2 and the Risk for Ovarian Cancer

Testing for Multiple Genetic Mutations via NGS for Patients: Very Strong Family History of Breast & Ovarian Cancer, Diagnosed at Young Ages, & Negative on BRCA Test

Posts Tagged ‘Conditions and Diseases’

The Vibrant Philly Biotech Scene: Focus on Computer-Aided Drug Design and Gfree Bio, LLC

Below is the interview with Dr. Reynolds of Gfree Bio LLC and Leaders in Pharmaceutical Business Intelligence (LPBI):

Also, if you would like your Philadelphia biotech startup to be highlighted in this series please contact me: sjwilliamspa@comcast.net or @StephenJWillia2.

Our site is read by ~ 570,000 readers, among them thousand international readers daily and followed by thousands of Twitter followers.

Other posts on this site in this VIBRANT PHILLY BIOTECH SCENE SERIES OR referring to PHILADELPHIA BIOTECH include:

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The Vibrant Philly Biotech Scene: Focus on Vaccines and Philimmune, LLC

Historic Timeline of Vaccine Development

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Prefacing the e-Book Epilogue: Metabolic Genomics and Pharmaceutics

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Twitter is Becoming a Powerful Tool in Science and Medicine

Twitter Analytics – measures metrics surrounding Tweets including retweets, impressions, engagement, follow rate, …

Examples of Twitter Use

A. Scientific Meeting Coverage

B. Twitter Usage for Patient Care and Engagement

C. Twitter Use in Pharmacovigilance to Monitor Adverse Events

D. Use of Twitter in Big Data Analytics

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Imaging-guided cancer treatment

Writer & reporter: Dror Nir, PhD

The following is dedicated to the role of imaging in guiding treatment.

Abstract

The challenges this review discusses

How imaging could mitigate the above mentioned challenges

Conclusions

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12. The Centrality of Ca(2+) Signaling and Cytoskeleton Involving Calmodulin Kinases and Ryanodine Receptors in Cardiac Failure, Arterial Smooth Muscle, Post-ischemic Arrhythmia, Similarities and Differences, and Pharmaceutical Targets

Author and Curator: Larry H Bernstein, MD, FCAP, Author, and Content Consultant to e-SERIES A: Cardiovascular Diseases: Justin Pearlman, MD, PhD, FACC and Curator: Aviva Lev-Ari, PhD, RN

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Dompe’ Receives FDA orphan drug designation for rhNGF in the treatment of Neurotrophic Keratitis (NK).

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Scientific Curation Fostering Expert Networks and Open Innovation: Lessons from Clive Thompson

Our ideas are PRODUCTS OF OUR ENVIRONMENT.

They are influenced by the conversations around us.

But HOW MUCH Knowledge is OUT THERE?

The Good, The Bad, and the Ugly of the Scientific Internet (The Wild West?)

So granted, there is a lot of

….. when it comes to scientific information on the internet!

Using Curation and Science 2.0 to build Trusted, Expert Networks of Scientists and Clinicians

In Summary: How Scientific Content Curation Can Help

CURATION MAY OFFER SOLUTIONS

Methodology in Scientific Content Curation as Envisioned by Aviva lev-Ari, PhD, RN

Cardiovascular Original Research: Cases in Methodology Design for Content Curation and Co-Curation

which has created a need for more context-driven scientific search and discourse.

INCREASE THE SCIENTIFIC CURRENCY.

Creating Content Curation Communities: Breaking Down the Silos!

Open Science Case Studies in Curation

How the Internet of Things is Promoting the Curation Effort

But this effort needs money

Future postings on the relevance and application of scientific curation will include:

Using Scientific Content Curation as a Method for Validation and Biocuration

Using Scientific Content Curation as a Method for Open Innovation

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Good and Bad News Reported for Ovarian Cancer Therapy

However FDA investigators voiced their skepticism of AstraZeneca’s clinical results, namely

This was certainly a disappointment as ….

PARP1 Inhibitors Currently in Clinical Trials for Ovarian Cancer

Summary of Combination Ovarian Cancer Trials with Avastin (current and closed)

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12. The Centrality of Ca(2+) Signaling and Cytoskeleton Involving Calmodulin Kinases and
Ryanodine Receptors in Cardiac Failure, Arterial Smooth Muscle, Post-ischemic Arrhythmia,
Similarities and Differences, and Pharmaceutical Targets

Author and Curator: Larry H Bernstein, MD, FCAP, Author, and Content Consultant to
e-SERIES A: Cardiovascular Diseases: Justin Pearlman, MD, PhD, FACC and
Curator: Aviva Lev-Ari, PhD, RN